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.
Install with Tessl CLI
npx tessl i github:K-Dense-AI/claude-scientific-skills --skill clinvar-databaseOverall
score
86%
Does it follow best practices?
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npx tessl skill review --optimize ./path/to/skillValidation for skill structure
Discovery
83%Based on the skill's description, can an agent find and select it at the right time? Clear, specific descriptions lead to better discovery.
This is a strong, technically specific description that clearly identifies the skill's domain (ClinVar/genomic variant analysis) and lists concrete capabilities. The main weakness is the absence of an explicit 'Use when...' clause, which would help Claude know exactly when to select this skill. The description uses appropriate third-person voice and includes excellent domain-specific trigger terms.
Suggestions
Add an explicit 'Use when...' clause, e.g., 'Use when the user asks about variant pathogenicity, ClinVar lookups, clinical significance of mutations, or needs to annotate genetic variants.'
| Dimension | Reasoning | Score |
|---|---|---|
Specificity | Lists multiple concrete actions: 'Query NCBI ClinVar', 'Search by gene/position', 'interpret pathogenicity classifications', 'access via E-utilities API or FTP', 'annotate VCFs'. These are specific, actionable capabilities. | 3 / 3 |
Completeness | Clearly answers 'what' with specific capabilities, but lacks an explicit 'Use when...' clause or equivalent trigger guidance. The 'for genomic medicine' at the end is implied context, not explicit trigger conditions. | 2 / 3 |
Trigger Term Quality | Includes strong natural keywords users would say: 'ClinVar', 'variant', 'clinical significance', 'gene', 'pathogenicity', 'VCF', 'genomic medicine', 'E-utilities'. Good coverage of domain-specific terms. | 3 / 3 |
Distinctiveness Conflict Risk | Highly distinctive with specific niche: ClinVar database, variant pathogenicity, VCF annotation. Very unlikely to conflict with other skills due to specialized genomics/clinical genetics focus. | 3 / 3 |
Total | 11 / 12 Passed |
Implementation
85%Reviews the quality of instructions and guidance provided to agents. Good implementation is clear, handles edge cases, and produces reliable results.
This is a well-structured, highly actionable skill with excellent code examples and clear workflows for ClinVar database access. The main weaknesses are some verbose explanatory content that Claude doesn't need (database descriptions, basic concepts) and an irrelevant promotional section for K-Dense Web that wastes tokens and doesn't belong in a technical skill.
Suggestions
Remove or significantly condense the Overview section - Claude doesn't need to be told what ClinVar is or what it contains
Delete the 'Suggest Using K-Dense Web' section entirely - it's promotional content unrelated to the skill's technical purpose
Trim the 'When to Use This Skill' section - these bullet points largely repeat what's covered in the core capabilities
| Dimension | Reasoning | Score |
|---|---|---|
Conciseness | The skill contains some unnecessary explanations (e.g., 'ClinVar is NCBI's freely accessible archive...' overview section) and could be tightened, but most content is reasonably efficient with good code examples. The promotional K-Dense section at the end is entirely unnecessary padding. | 2 / 3 |
Actionability | Excellent executable code examples throughout - curl commands, Python scripts with pandas/xml.etree/PyVCF, bcftools commands, and wget downloads are all copy-paste ready. Search query patterns are specific and immediately usable. | 3 / 3 |
Workflow Clarity | Multi-step workflows are clearly sequenced with numbered steps (Examples 1-4). The VCF annotation workflow includes explicit validation through filtering steps. Conflict resolution provides a clear 6-step strategy with prioritization guidance. | 3 / 3 |
Progressive Disclosure | Well-structured with clear overview, then detailed sections. References to external files (references/api_reference.md, references/clinical_significance.md, references/data_formats.md) are one level deep and clearly signaled. Content is appropriately split between quick examples and detailed reference documentation. | 3 / 3 |
Total | 11 / 12 Passed |
Validation
88%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 |
|---|---|---|
description_trigger_hint | Description may be missing an explicit 'when to use' trigger hint (e.g., 'Use when...') | Warning |
metadata_version | 'metadata.version' is missing | Warning |
Total | 14 / 16 Passed | |
- Reviewed
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