clinvar-database

Query NCBI ClinVar for variant clinical significance. Search by gene/position, interpret pathogenicity classifications, access via E-utilities API or FTP, annotate VCFs, for genomic medicine.

Quality

77%

Does it follow best practices?

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Securityby

Low

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tessl review fix ./backend/cli/skills/databases/clinvar-database/SKILL.md

Quality

Content

72%

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

A thorough, highly actionable ClinVar reference with strong progressive disclosure and executable examples, weakened by some redundant background prose and missing validation checkpoints in its batch workflows. Solid overall with room to tighten and add verification steps.

Suggestions

Trim the Overview and ACMG/AMP explanatory prose that Claude already knows; keep only ClinVar-specific operational detail.

Add explicit validation/verification steps to the batch workflows (e.g., verify annotated VCF integrity, confirm database record counts after load) so workflow clarity can reach 3.

Consolidate the redundant file-format listings between the body and the data_formats reference to reduce token cost.

Dimension	Reasoning	Score
Conciseness	Mostly efficient operational detail, but the Overview explains what ClinVar is and the classifications section restates general ACMG/AMP knowledge Claude already has; the body could be tightened throughout.	2 / 3
Actionability	Provides copy-paste-ready, executable guidance — curl E-utilities calls, bcftools annotate/view commands, Python xml.etree and pandas snippets, and awk one-liners.	3 / 3
Workflow Clarity	Workflows are numbered and sequenced, but batch/destructive operations (VCF annotation, bulk database construction) lack explicit validation checkpoints, capping workflow clarity at 2.	2 / 3
Progressive Disclosure	The body is a well-signaled overview that delegates detail to real one-level-deep references (api_reference.md, clinical_significance.md, data_formats.md), all of which exist in ./references/.	3 / 3
	Total	10 / 12 Passed

Description

82%

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 specific, well-targeted description that names concrete ClinVar actions and natural trigger terms, but it omits an explicit 'Use when' activation clause, capping completeness at 2. Overall a strong description with one clear gap.

Suggestions

Add an explicit activation clause such as 'Use when querying variant clinical significance in ClinVar, annotating VCFs with pathogenicity, or accessing ClinVar via E-utilities/FTP.'

Clarify the 'when' context beyond the domain tag 'for genomic medicine' so Claude knows precisely when to invoke this skill.

Dimension	Reasoning	Score
Specificity	Lists multiple concrete actions — 'Search by gene/position, interpret pathogenicity classifications, access via E-utilities API or FTP, annotate VCFs' — rather than vague language.	3 / 3
Completeness	Clearly answers 'what' the skill does, but lacks an explicit 'Use when...' trigger clause; 'for genomic medicine' is domain context, not activation guidance, so completeness is capped at 2.	2 / 3
Trigger Term Quality	Uses natural domain terms a genomics user would actually say — 'ClinVar', 'variant clinical significance', 'pathogenicity', 'VCFs', 'gene' — with good coverage of common variations.	3 / 3
Distinctiveness Conflict Risk	ClinVar-specific niche with distinct triggers (ClinVar, E-utilities, VCF annotation) unlikely to collide with other skills.	3 / 3
	Total	11 / 12 Passed

Validation

87%

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 — 14 / 16 Passed

Validation for skill structure

Criteria	Description	Result
metadata_version	'metadata.version' is missing	Warning
frontmatter_unknown_keys	Unknown frontmatter key(s) found; consider removing or moving to metadata	Warning

	Total	14 / 16 Passed

Repository: synthetic-sciences/openscience
Path: backend/cli/skills/databases/clinvar-database/SKILL.md
Commit: 52845c3

Reviewed: about 10 hours ago

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