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

Low-risk findings worth noting

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

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 and well-structured for progressive disclosure, with concrete executable examples and clean reference file separation. Its weaknesses are minor repetition across best-practices sections and the absence of validation checkpoints in the batch-operation workflow examples.

Suggestions

Add explicit validation checkpoints to the batch/destructive workflows — e.g. verify downloaded file integrity (size/checksum), confirm bcftools annotate succeeded before filtering, and validate DB row counts after load.

De-duplicate the "Critical considerations", "Best practices", and Overview lists, which repeat points already made in the numbered capability sections.

Consolidate the per-section "Best practices" bullets into a single concise checklist to reduce token overhead.

Dimension	Reasoning	Score
Conciseness	The body is mostly efficient — tight lists and executable code blocks with no padding of basic concepts — but the "Critical considerations", "Best practices", and Overview sections repeat points made elsewhere and could be trimmed.	4 / 5
Actionability	Fully executable, copy-paste-ready guidance throughout: concrete curl/wget/bcftools commands, complete Python snippets (xml.etree iterparse, pandas filtering, vcf reader), and specific search-query syntax covering the common cases.	5 / 5
Workflow Clarity	The four worked examples provide clear numbered sequences, but they involve batch/destructive operations (bulk download, VCF annotation, database construction) with no explicit validation checkpoints, which caps workflow clarity at 3 per the rubric.	3 / 5
Progressive Disclosure	The SKILL.md is a clear overview that signals three real one-level-deep references (api_reference.md, clinical_significance.md, data_formats.md) in context and in a Resources section, with bulk detail appropriately split into those files.	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, actionable, and distinctive, with strong concrete verbs and good trigger keywords. Its main weakness is the absence of an explicit "Use when..." clause, leaving the trigger conditions implicit.

Suggestions

Add an explicit "Use when..." clause (e.g. "Use when querying variant clinical significance in ClinVar, annotating VCFs, or resolving conflicting pathogenicity calls") to satisfy the 'when' half of completeness.

Include natural synonyms and file extensions (e.g. ".vcf", "germline variants", "star ratings") to broaden trigger-term coverage.

Reframe "for genomic medicine" as a concrete trigger phrase rather than a trailing context tag.

Dimension	Reasoning	Score
Specificity	The description lists multiple concrete actions — "Query NCBI ClinVar", "Search by gene/position", "interpret pathogenicity classifications", "access via E-utilities API or FTP", "annotate VCFs" — giving comprehensive coverage of distinct capabilities.	5 / 5
Completeness	It clearly states "what" the skill does but has no explicit "Use when..." trigger guidance — "for genomic medicine" is a vague context tag, not a concrete when-clause, which caps completeness at 3 per the rubric.	3 / 5
Trigger Term Quality	Solid domain keywords a genomics user would say ("variant clinical significance", "pathogenicity classifications", "E-utilities API", "annotate VCFs"), but some natural synonyms and file extensions (e.g. ".vcf", "germline", "star ratings") are missing.	4 / 5
Distinctiveness Conflict Risk	"NCBI ClinVar for variant clinical significance" with E-utilities/VCF annotation defines a clear niche with distinct triggers and minimal overlap with other skills.	5 / 5
	Total	17 / 20 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: 3a6c3a9

Reviewed: 1 day ago

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