annotating-variants

Annotates VCF variants and normalizes HGVS nomenclature with public, license-free annotators (Ensembl VEP REST, VEP/SnpEff/ANNOVAR offline) and links variants to gnomAD population frequencies and the clinical context OpenMed extracts. Use when the user wants to predict variant consequences, map HGVS to genomic coordinates, annotate a VCF, attach allele frequencies, or pair variants with phenotype/oncology context. Trigger keywords: VCF, HGVS, variant annotation, VEP, SnpEff, ANNOVAR, consequence, missense, gnomAD, allele frequency, GRCh38, rsID, transcript. Pairs adjacent to OpenMed: combine annotated variants with Genomics/Oncology entities and phenotype from openmed.analyze_text. Tools used are free; restricted clinical databases are user-supplied.

Quality

88%

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Passed

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Quality

Content

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

The body is actionable and well-structured with executable code throughout, but its workflow lacks explicit validation checkpoints for a batch operation, which the rubric caps at 3, and a little framing prose keeps conciseness just below the top anchor.

Suggestions

Add an explicit validation step to the Workflow (e.g. after annotating, verify consequence fields populated and retry on 429/empty responses) to lift workflow_clarity above the batch-operation cap of 3.

Trim framing prose like "The workhorse for a quick, no-install annotation is..." and consolidate the license paragraph so the body leads directly with the executable guidance.

Consider moving the offline-annotator comparison table and standards list into a short reference file if the skill grows, to keep SKILL.md as a lean overview.

Dimension	Reasoning	Score
Conciseness	Mostly efficient with executable code front and center, but framing prose such as "The workhorse for a quick, no-install annotation is the Ensembl VEP REST API" and the license paragraph could be trimmed; not quite the lean top anchor.	4 / 5
Actionability	Provides copy-paste-ready Python for VEP REST GET/POST, a gnomAD GraphQL query, and an equivalent cURL command, with a concrete TP53 example covering the common cases.	5 / 5
Workflow Clarity	A clear five-step sequence (normalize → annotate → attach frequencies → filter → join) is present, but there are no explicit validation checkpoints or validate→fix→retry feedback loops, and for a batch-annotation task the rubric caps this at 3.	3 / 5
Progressive Disclosure	Well-organized into labeled sections (When to use, Quick start, Population frequencies, Offline annotation, Workflow, Hand-off, Edge cases, Standards & references) with clear one-level external URL references and no nested file hops, though it is a fairly long single file.	4 / 5
	Total	16 / 20 Passed

Description

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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 third-person, specific, and comprehensive: it states concrete actions, names the annotators and data sources, and gives an explicit "Use when" trigger clause with a keyword list. It cleanly hits the top anchor on every dimension.

Dimension	Reasoning	Score
Specificity	Lists multiple concrete actions — "Annotates VCF variants", "normalizes HGVS nomenclature", "links variants to gnomAD population frequencies", "pair variants with phenotype/oncology context" — with named annotators, giving comprehensive coverage.	5 / 5
Completeness	Clearly answers both what (annotate/normalize/link/pair) and when via an explicit "Use when the user wants to..." clause with concrete trigger phrases, matching the top anchor.	5 / 5
Trigger Term Quality	Includes an explicit trigger-keyword list with natural terms and synonyms users say — VCF, HGVS, VEP, SnpEff, ANNOVAR, gnomAD, allele frequency, GRCh38, rsID, missense — plus file/format variations.	5 / 5
Distinctiveness Conflict Risk	Occupies a clear niche (variant annotation + HGVS normalization with named open tools) and signals adjacency to OpenMed, so it is unlikely to trigger for unrelated skills.	5 / 5
	Total	20 / 20 Passed

Validation

100%

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 — 16 / 16 Passed

Validation for skill structure

No warnings or errors.

Repository: maziyarpanahi/openmed
Path: skills/annotating-variants/SKILL.md
Commit: 80da98c

Reviewed: 1 day ago

Table of Contents

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