Skill · em Dados, IA e pesquisa

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.

Procedência

Antes de instalar

4 arquivos · 38,9 KB · só texto, nenhum script

Instalar na sua CLI

O comando baixa a versão fixada (commit 57f899e) direto da origem, para a pasta que a CLI lê. Precisa de curl (macOS e Linux); no Windows não há comando, porque o Rook Labs é para macOS.

Claude Code

Neste projeto: instala em .claude/skills/clinvar-database/.

d=".claude/skills/clinvar-database"
u="https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/cli-tool/components/skills/scientific/clinvar-database"
curl -fsSL --create-dirs \
  -o "$d/SKILL.md" "$u/SKILL.md" \
  -o "$d/references/api_reference.md" "$u/references/api_reference.md" \
  -o "$d/references/clinical_significance.md" "$u/references/clinical_significance.md" \
  -o "$d/references/data_formats.md" "$u/references/data_formats.md" \
  -o "$d/LICENSE" "https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/LICENSE"

Global: instala em ~/.claude/skills/clinvar-database/.

d="$HOME/.claude/skills/clinvar-database"
u="https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/cli-tool/components/skills/scientific/clinvar-database"
curl -fsSL --create-dirs \
  -o "$d/SKILL.md" "$u/SKILL.md" \
  -o "$d/references/api_reference.md" "$u/references/api_reference.md" \
  -o "$d/references/clinical_significance.md" "$u/references/clinical_significance.md" \
  -o "$d/references/data_formats.md" "$u/references/data_formats.md" \
  -o "$d/LICENSE" "https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/LICENSE"

Codex

Neste projeto: instala em .agents/skills/clinvar-database/.

d=".agents/skills/clinvar-database"
u="https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/cli-tool/components/skills/scientific/clinvar-database"
curl -fsSL --create-dirs \
  -o "$d/SKILL.md" "$u/SKILL.md" \
  -o "$d/references/api_reference.md" "$u/references/api_reference.md" \
  -o "$d/references/clinical_significance.md" "$u/references/clinical_significance.md" \
  -o "$d/references/data_formats.md" "$u/references/data_formats.md" \
  -o "$d/LICENSE" "https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/LICENSE"

Global: instala em ~/.agents/skills/clinvar-database/.

d="$HOME/.agents/skills/clinvar-database"
u="https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/cli-tool/components/skills/scientific/clinvar-database"
curl -fsSL --create-dirs \
  -o "$d/SKILL.md" "$u/SKILL.md" \
  -o "$d/references/api_reference.md" "$u/references/api_reference.md" \
  -o "$d/references/clinical_significance.md" "$u/references/clinical_significance.md" \
  -o "$d/references/data_formats.md" "$u/references/data_formats.md" \
  -o "$d/LICENSE" "https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/LICENSE"

Antigravity

Neste projeto: instala em .agents/skills/clinvar-database/.

d=".agents/skills/clinvar-database"
u="https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/cli-tool/components/skills/scientific/clinvar-database"
curl -fsSL --create-dirs \
  -o "$d/SKILL.md" "$u/SKILL.md" \
  -o "$d/references/api_reference.md" "$u/references/api_reference.md" \
  -o "$d/references/clinical_significance.md" "$u/references/clinical_significance.md" \
  -o "$d/references/data_formats.md" "$u/references/data_formats.md" \
  -o "$d/LICENSE" "https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/LICENSE"

Global: instala em ~/.gemini/antigravity-cli/skills/clinvar-database/.

d="$HOME/.gemini/antigravity-cli/skills/clinvar-database"
u="https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/cli-tool/components/skills/scientific/clinvar-database"
curl -fsSL --create-dirs \
  -o "$d/SKILL.md" "$u/SKILL.md" \
  -o "$d/references/api_reference.md" "$u/references/api_reference.md" \
  -o "$d/references/clinical_significance.md" "$u/references/clinical_significance.md" \
  -o "$d/references/data_formats.md" "$u/references/data_formats.md" \
  -o "$d/LICENSE" "https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/LICENSE"

Peça ao Rook

Já usa o Rook Labs? Cole no chat do Rook: instale a skill https://rooklabs.sh/marketplace/cct.clinvar-database

Prévia do SKILL.md

---
name: clinvar-database
description: "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."
---

# ClinVar Database

## Overview

ClinVar is NCBI's freely accessible archive of reports on relationships between human genetic variants and phenotypes, with supporting evidence. The database aggregates information about genomic variation and its relationship to human health, providing standardized variant classifications used in clinical genetics and …

## When to Use This Skill

This skill should be used when:

- Searching for variants by gene, condition, or clinical significance
- Interpreting clinical significance classifications (pathogenic, benign, VUS)
- Accessing ClinVar data programmatically via E-utilities API
- Downloading and processing bulk data from FTP
- Understanding review status and star ratings
- Resolving conflicting variant interpretations
- Annotating variant call sets with clinical significance

## Core Capabilities

### 1. Search and Query ClinVar

#### Web Interface Queries

Search ClinVar using the web interface at https://www.ncbi.nlm.nih.gov/clinvar/

**Common search patterns:**
- By gene: `BRCA1[gene]`
- By clinical significance: `pathogenic[CLNSIG]`
- By condition: `breast cancer[disorder]`
- By variant: `NM_000059.3:c.1310_1313del[variant name]`
- By chromosome: `13[chr]`
- Combined: `BRCA1[gene] AND pathogenic[CLNSIG]`

#### Programmatic Access via E-utilities
…

Ver todo o marketplace