gwas-database

Query NHGRI-EBI GWAS Catalog for SNP-trait associations. Search variants by rs ID, disease/trait, gene, retrieve p-values and summary statistics, for genetic epidemiology and polygenic risk scores.

Quality

73%

Does it follow best practices?

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Securityby

Low

Low-risk findings worth noting

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tessl review fix ./scientific-skills/Evidence Insight/gwas-database/SKILL.md

Quality

Content

71%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 content is highly actionable with executable examples and well-sequenced workflows, but is over-long for a single file, contains promotional padding, and references a non-existent api_reference.md bundle file.

Suggestions

Move bulk reference material (response field schemas, Best Practices, Limitations, full endpoint catalog) into a real references/api_reference.md file so SKILL.md becomes a lean overview with one-level-deep pointers.

Remove the promotional "Suggest Using K-Dense Web" section and de-duplicate the URL lists ("Additional Resources" repeats URLs already given in earlier sections).

Add validation checkpoints to Workflows 2–5 (e.g., confirm non-200 responses, verify EFO/gene IDs resolve) to match the feedback-loop standard set in Workflow 1.

Dimension	Reasoning	Score
Conciseness	The ~620-line body is mostly efficient — concrete API examples and field references earn their place — but contains padded sections (the promotional "Suggest Using K-Dense Web" block, duplicated URL lists in "Additional Resources", and verbose Best Practices/Limitations notes) that could be tightened.	3 / 5
Actionability	Provides fully executable, copy-paste-ready Python (requests calls, paginated query function with rate limiting, wget downloads) covering the common cases — variant, trait, gene, region, and summary-statistics queries.	5 / 5
Workflow Clarity	Five numbered workflows are clearly sequenced, and Workflow 1 includes an explicit checkpoint and a feedback loop (non-200 handling, retry with alternative trait IDs, web fallback); minor validation gaps exist in Workflows 2–5, which are read-only analyses rather than destructive operations.	4 / 5
Progressive Disclosure	Good section headers provide structure, but the skill is monolithic at ~620 lines with all reference material inline, and the "references/api_reference.md" pointer targets a file that does not exist in the bundle (no references/, scripts/, or assets/ directories present).	3 / 5
	Total	15 / 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, actionable, and well-differentiated, but lacks an explicit "Use when..." trigger clause, leaving the invocation conditions only weakly implied.

Suggestions

Add an explicit trigger clause such as "Use when querying GWAS Catalog for SNP-trait associations, variant lookups by rs ID, or retrieving p-values and summary statistics."

Include a few more natural synonyms users might say (e.g., "GWAS hits", "genome-wide associations", "risk variants") to broaden trigger coverage.

Dimension	Reasoning	Score
Specificity	Lists multiple concrete actions — "Query NHGRI-EBI GWAS Catalog", "Search variants by rs ID, disease/trait, gene", "retrieve p-values and summary statistics" — giving comprehensive coverage of capabilities rather than vague language.	5 / 5
Completeness	The "what" is clear (query/search/retrieve actions) but the "when" is only weakly implied via the purpose clause "for genetic epidemiology and polygenic risk scores"; there is no explicit "Use when..." trigger clause, which caps completeness at 3 per the guidelines.	3 / 5
Trigger Term Quality	Strong natural keyword coverage ("SNP-trait associations", "rs ID", "disease/trait", "gene", "p-values", "summary statistics", "polygenic risk scores") that researchers would say, though a few common variants like "GWAS", "variant", or "genome-wide" are absent and no file extensions apply to this database-query domain.	4 / 5
Distinctiveness Conflict Risk	Targets a specific named resource (NHGRI-EBI GWAS Catalog) with SNP-trait association triggers, occupying a clear niche with minimal overlap risk against other skills.	5 / 5
	Total	17 / 20 Passed

Validation

81%

Warnings & errors only

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

Criteria	Description	Result
skill_md_line_count	SKILL.md is long (629 lines); consider splitting into references/ and linking	Warning
frontmatter_unknown_keys	Unknown frontmatter key(s) found; consider removing or moving to metadata	Warning
referenced_paths_exist	Referenced path issues: 1 missing	Warning

	Total	13 / 16 Passed

Repository: aipoch/medical-research-skills
Path: scientific-skills/Evidence Insight/gwas-database/SKILL.md
Commit: 63c61d3

Reviewed: 8 hours ago

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