Skill · em Dados, IA e pesquisa

bioservices

Primary Python tool for 40+ bioinformatics services. Preferred for multi-database workflows: UniProt, KEGG, ChEMBL, PubChem, Reactome, QuickGO. Unified API for queries, ID mapping, pathway analysis. For direct REST control, use individual database skills (uniprot-database, kegg-database).

Procedência

Origem: davila7/claude-code-templates
Caminho: cli-tool/components/skills/scientific/bioservices
Versão fixada: 57f899e5394bb8ca166f38eacae8f0853cbfe033
Licença: MIT
Espelhado em 25/09/2026
nenhum download no Claude Code Templates (lido em 25/09/2026)

Antes de instalar

8 arquivos · 101,8 KB · inclui 4 scripts que executam: scripts/batch_id_converter.py, scripts/compound_cross_reference.py, scripts/pathway_analysis.py, scripts/protein_analysis_workflow.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/bioservices/.

d=".claude/skills/bioservices"
u="https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/cli-tool/components/skills/scientific/bioservices"
curl -fsSL --create-dirs \
  -o "$d/SKILL.md" "$u/SKILL.md" \
  -o "$d/references/identifier_mapping.md" "$u/references/identifier_mapping.md" \
  -o "$d/references/services_reference.md" "$u/references/services_reference.md" \
  -o "$d/references/workflow_patterns.md" "$u/references/workflow_patterns.md" \
  -o "$d/scripts/batch_id_converter.py" "$u/scripts/batch_id_converter.py" \
  -o "$d/scripts/compound_cross_reference.py" "$u/scripts/compound_cross_reference.py" \
  -o "$d/scripts/pathway_analysis.py" "$u/scripts/pathway_analysis.py" \
  -o "$d/scripts/protein_analysis_workflow.py" "$u/scripts/protein_analysis_workflow.py" \
  -o "$d/LICENSE" "https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/LICENSE"

Global: instala em ~/.claude/skills/bioservices/.

d="$HOME/.claude/skills/bioservices"
u="https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/cli-tool/components/skills/scientific/bioservices"
curl -fsSL --create-dirs \
  -o "$d/SKILL.md" "$u/SKILL.md" \
  -o "$d/references/identifier_mapping.md" "$u/references/identifier_mapping.md" \
  -o "$d/references/services_reference.md" "$u/references/services_reference.md" \
  -o "$d/references/workflow_patterns.md" "$u/references/workflow_patterns.md" \
  -o "$d/scripts/batch_id_converter.py" "$u/scripts/batch_id_converter.py" \
  -o "$d/scripts/compound_cross_reference.py" "$u/scripts/compound_cross_reference.py" \
  -o "$d/scripts/pathway_analysis.py" "$u/scripts/pathway_analysis.py" \
  -o "$d/scripts/protein_analysis_workflow.py" "$u/scripts/protein_analysis_workflow.py" \
  -o "$d/LICENSE" "https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/LICENSE"

Codex

Neste projeto: instala em .agents/skills/bioservices/.

d=".agents/skills/bioservices"
u="https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/cli-tool/components/skills/scientific/bioservices"
curl -fsSL --create-dirs \
  -o "$d/SKILL.md" "$u/SKILL.md" \
  -o "$d/references/identifier_mapping.md" "$u/references/identifier_mapping.md" \
  -o "$d/references/services_reference.md" "$u/references/services_reference.md" \
  -o "$d/references/workflow_patterns.md" "$u/references/workflow_patterns.md" \
  -o "$d/scripts/batch_id_converter.py" "$u/scripts/batch_id_converter.py" \
  -o "$d/scripts/compound_cross_reference.py" "$u/scripts/compound_cross_reference.py" \
  -o "$d/scripts/pathway_analysis.py" "$u/scripts/pathway_analysis.py" \
  -o "$d/scripts/protein_analysis_workflow.py" "$u/scripts/protein_analysis_workflow.py" \
  -o "$d/LICENSE" "https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/LICENSE"

Global: instala em ~/.agents/skills/bioservices/.

d="$HOME/.agents/skills/bioservices"
u="https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/cli-tool/components/skills/scientific/bioservices"
curl -fsSL --create-dirs \
  -o "$d/SKILL.md" "$u/SKILL.md" \
  -o "$d/references/identifier_mapping.md" "$u/references/identifier_mapping.md" \
  -o "$d/references/services_reference.md" "$u/references/services_reference.md" \
  -o "$d/references/workflow_patterns.md" "$u/references/workflow_patterns.md" \
  -o "$d/scripts/batch_id_converter.py" "$u/scripts/batch_id_converter.py" \
  -o "$d/scripts/compound_cross_reference.py" "$u/scripts/compound_cross_reference.py" \
  -o "$d/scripts/pathway_analysis.py" "$u/scripts/pathway_analysis.py" \
  -o "$d/scripts/protein_analysis_workflow.py" "$u/scripts/protein_analysis_workflow.py" \
  -o "$d/LICENSE" "https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/LICENSE"

Antigravity

Neste projeto: instala em .agents/skills/bioservices/.

d=".agents/skills/bioservices"
u="https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/cli-tool/components/skills/scientific/bioservices"
curl -fsSL --create-dirs \
  -o "$d/SKILL.md" "$u/SKILL.md" \
  -o "$d/references/identifier_mapping.md" "$u/references/identifier_mapping.md" \
  -o "$d/references/services_reference.md" "$u/references/services_reference.md" \
  -o "$d/references/workflow_patterns.md" "$u/references/workflow_patterns.md" \
  -o "$d/scripts/batch_id_converter.py" "$u/scripts/batch_id_converter.py" \
  -o "$d/scripts/compound_cross_reference.py" "$u/scripts/compound_cross_reference.py" \
  -o "$d/scripts/pathway_analysis.py" "$u/scripts/pathway_analysis.py" \
  -o "$d/scripts/protein_analysis_workflow.py" "$u/scripts/protein_analysis_workflow.py" \
  -o "$d/LICENSE" "https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/LICENSE"

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

d="$HOME/.gemini/antigravity-cli/skills/bioservices"
u="https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/cli-tool/components/skills/scientific/bioservices"
curl -fsSL --create-dirs \
  -o "$d/SKILL.md" "$u/SKILL.md" \
  -o "$d/references/identifier_mapping.md" "$u/references/identifier_mapping.md" \
  -o "$d/references/services_reference.md" "$u/references/services_reference.md" \
  -o "$d/references/workflow_patterns.md" "$u/references/workflow_patterns.md" \
  -o "$d/scripts/batch_id_converter.py" "$u/scripts/batch_id_converter.py" \
  -o "$d/scripts/compound_cross_reference.py" "$u/scripts/compound_cross_reference.py" \
  -o "$d/scripts/pathway_analysis.py" "$u/scripts/pathway_analysis.py" \
  -o "$d/scripts/protein_analysis_workflow.py" "$u/scripts/protein_analysis_workflow.py" \
  -o "$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.bioservices

Prévia do SKILL.md

---
name: bioservices
description: "Primary Python tool for 40+ bioinformatics services. Preferred for multi-database workflows: UniProt, KEGG, ChEMBL, PubChem, Reactome, QuickGO. Unified API for queries, ID mapping, pathway analysis. For direct REST control, use individual database skills (uniprot-database, kegg-database)."
---

# BioServices

## Overview

BioServices is a Python package providing programmatic access to approximately 40 bioinformatics web services and databases. Retrieve biological data, perform cross-database queries, map identifiers, analyze sequences, and integrate multiple biological resources in Python workflows. The package handles both REST and SO…

## When to Use This Skill

This skill should be used when:
- Retrieving protein sequences, annotations, or structures from UniProt, PDB, Pfam
- Analyzing metabolic pathways and gene functions via KEGG or Reactome
- Searching compound databases (ChEBI, ChEMBL, PubChem) for chemical information
- Converting identifiers between different biological databases (KEGG↔UniProt, compound IDs)
- Running sequence similarity searches (BLAST, MUSCLE alignment)
- Querying gene ontology terms (QuickGO, GO annotations)
- Accessing protein-protein interaction data (PSICQUIC, IntactComplex)
- Mining genomic data (BioMart, ArrayExpress, ENA)
- Integrating data from multiple bioinformatics resources in a single workflow

## Core Capabilities

### 1. Protein Analysis

Retrieve protein information, sequences, and functional annotations:

```python
from bioservices import UniProt

u = UniProt(verbose=False)

# Search for protein by name
results = u.search("ZAP70_HUMAN", frmt="tab", columns="id,genes,organism")

# Retrieve FASTA sequence
sequence = u.retrieve("P43403", "fasta")
…

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