alterlab-bioservices

Unify access to 40 bioinformatics services via a single Python interface.

58|9|Updated Mar 16, 2026

Search Tags:#bioinformatics #pathways #mapping #batch-processing #bioservices #GO #protein

Ready to run

npx skills add https://github.com/AlterLab-IEU/AlterLab-Academic-Skills --skill alterlab-bioservices

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: alterlab-bioservices
Source: https://github.com/AlterLab-IEU/AlterLab-Academic-Skills/tree/main/skills/bioinformatics/alterlab-bioservices
Command: npx skills add https://github.com/AlterLab-IEU/AlterLab-Academic-Skills --skill alterlab-bioservices

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires bioservices, and includes scripts (resource) and references (resource) components.

What problem does it solve?

Cross-database research in bioinformatics is fragmented across many services; this Skill provides a single Python interface to access ~40 web services for integrated queries and workflows.

Core Features & Use Cases

Unified access to protein, gene, pathway, compound, and GO data across multiple resources via bioservices.
Batch processing & robust workflows: map identifiers, fetch sequences, and analyze pathways in batch with error handling and retry strategies.
Use Case: researchers can map UniProt IDs to KEGG, retrieve GO annotations, and discover related pathways in one cohesive script.

Quick Start

Install the bioservices package and run one of the example workflows, e.g., execute scripts/protein_analysis_workflow.py with a target protein ID.

Frequently Asked Questions about alterlab-bioservices

High-intent search queries and answers about installing and using this skill.

FAQPage Schema

How do I map UniProt IDs to KEGG pathways in batch with error handling?▼

You can map UniProt IDs to KEGG and retrieve pathway data in batch using a single Python interface that unifies roughly 40 bioinformatics web services, incorporating error handling and retry strategies for robust cross-database workflows.

What is the best way to query multiple bioinformatics databases for protein and gene annotations?▼

The best way to query multiple databases is using a unified Python interface that connects to about 40 bioinformatics services, enabling you to fetch sequences, retrieve GO annotations, and aggregate data across resources in one cohesive script.

Do I need the bioservices library and Python 3 to run cross-database bioinformatics queries?▼

Yes, you need the bioservices library, Python 3, and network access to run cross-database bioinformatics queries. This setup supports batch workflows, identifier mapping, and data aggregation across the connected web services.

Can I retrieve GO annotations and discover related pathways using a single bioinformatics script?▼

Yes, you can retrieve GO annotations and discover related pathways in a single script. The interface unifies access to multiple resources, allowing you to perform protein analysis, gene identifier mapping, and pathway discovery cohesively.

How does cross-database identifier mapping work for compounds and interaction networks?▼

Cross-database identifier mapping works by querying a unified Python interface that accesses approximately 40 web services, allowing you to cross-reference compounds, map protein and gene identifiers, and analyze interaction networks across multiple resources.