Skill · em Dados, IA e pesquisa

ensembl-database

Query Ensembl genome database REST API for 250+ species. Gene lookups, sequence retrieval, variant analysis, comparative genomics, orthologs, VEP predictions, for genomic research.

Procedência

Antes de instalar

3 arquivos · 31,1 KB · inclui 1 script que executa: scripts/ensembl_query.py

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/ensembl-database/.

d=".claude/skills/ensembl-database"
u="https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/cli-tool/components/skills/scientific/ensembl-database"
curl -fsSL --create-dirs \
  -o "$d/SKILL.md" "$u/SKILL.md" \
  -o "$d/references/api_endpoints.md" "$u/references/api_endpoints.md" \
  -o "$d/scripts/ensembl_query.py" "$u/scripts/ensembl_query.py" \
  -o "$d/LICENSE" "https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/LICENSE"

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

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

Codex

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

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

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

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

Antigravity

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

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

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

d="$HOME/.gemini/antigravity-cli/skills/ensembl-database"
u="https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/cli-tool/components/skills/scientific/ensembl-database"
curl -fsSL --create-dirs \
  -o "$d/SKILL.md" "$u/SKILL.md" \
  -o "$d/references/api_endpoints.md" "$u/references/api_endpoints.md" \
  -o "$d/scripts/ensembl_query.py" "$u/scripts/ensembl_query.py" \
  -o "$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.ensembl-database

Prévia do SKILL.md

---
name: ensembl-database
description: "Query Ensembl genome database REST API for 250+ species. Gene lookups, sequence retrieval, variant analysis, comparative genomics, orthologs, VEP predictions, for genomic research."
---

# Ensembl Database

## Overview

Access and query the Ensembl genome database, a comprehensive resource for vertebrate genomic data maintained by EMBL-EBI. The database provides gene annotations, sequences, variants, regulatory information, and comparative genomics data for over 250 species. Current release is 115 (September 2025).

## When to Use This Skill

This skill should be used when:

- Querying gene information by symbol or Ensembl ID
- Retrieving DNA, transcript, or protein sequences
- Analyzing genetic variants using the Variant Effect Predictor (VEP)
- Finding orthologs and paralogs across species
- Accessing regulatory features and genomic annotations
- Converting coordinates between genome assemblies (e.g., GRCh37 to GRCh38)
- Performing comparative genomics analyses
- Integrating Ensembl data into genomic research pipelines

## Core Capabilities

### 1. Gene Information Retrieval

Query gene data by symbol, Ensembl ID, or external database identifiers.

**Common operations:**
- Look up gene information by symbol (e.g., "BRCA2", "TP53")
- Retrieve transcript and protein information
- Get gene coordinates and chromosomal locations
- Access cross-references to external databases (UniProt, RefSeq, etc.)

**Using the ensembl_rest package:**
```python
from ensembl_rest import EnsemblClient
…

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