bioservices

Orchestrates BioServices to map identifiers and retrieve biological data across databases.

48|6|Updated Mar 9, 2026
One-click install
npx skills add https://github.com/qinyan-ai/qinyan-academic-skills --skill bioservices-qinyan-ai
Or copy as Structured Prompt for Agent
Please help me install this Agent Skill.
Skill: bioservices
Source: https://github.com/qinyan-ai/qinyan-academic-skills/tree/main/skills/05-%E7%94%9F%E7%89%A9%E4%BF%A1%E6%81%AF%E4%B8%8E%E5%9F%BA%E5%9B%A0%E7%BB%84%E5%AD%A6/bioservices
Command: npx skills add https://github.com/qinyan-ai/qinyan-academic-skills --skill bioservices-qinyan-ai

SYSTEM DOCUMENTATION & REQUIREMENTS

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

What problem does it solve?

Programmers and researchers need to orchestrate cross-database bioinformatics queries and identifier mappings across many services; this Skill provides a unified Python interface to BioServices, enabling seamless data retrieval and workflow automation.

Core Features & Use Cases

  • Cross-database identifier mapping (e.g., UniProt ↔ KEGG, GO, Ensembl, ChEMBL, ChEBI)
  • Multi-service workflows for proteins and compounds (UniProt, KEGG, PSICQUIC, GO annotations, ChEBI/ChEMBL)
  • Batch processing and pipeline automation for proteomics and genomics tasks
  • Example: map a UniProt entry to KEGG, fetch pathways, and retrieve GO terms in a single script.

Quick Start

Run a basic workflow that maps a UniProt ID to KEGG, retrieves GO annotations, and fetches KEGG pathways.

Frequently Asked Questions about bioservices

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

FAQPage Schema
How do I map UniProt identifiers to KEGG pathways and retrieve GO annotations in a single script?

You can map UniProt identifiers to KEGG and retrieve GO annotations by orchestrating cross-database queries through a unified Python interface. This approach enables multi-service workflows for proteins, fetching pathways and GO terms within a single batch processing script.

What is the best way to perform cross-database biological data retrieval for small molecules?

Cross-database biological data retrieval for small molecules is best handled by querying ChEBI and ChEMBL cross-references together. A unified Python interface allows seamless compound data retrieval and identifier mapping across these services with robust error handling.

Does batch processing for proteomics identifier mapping require the bioservices Python library?

Yes, batch processing for proteomics identifier mapping requires the bioservices library and Python 3.x. The environment supports automated mapping pipelines and script-based batch processing for cross-database workflows like UniProt to KEGG mapping.

Can I integrate PSICQUIC interaction data with UniProt and ChEMBL workflows?

Yes, you can integrate PSICQUIC interaction data with UniProt and ChEMBL workflows. The unified interface orchestrates multi-service integration, allowing protein-centric workflows to combine interaction data with GO annotations and small-molecule cross-references.

How does cross-database identifier mapping handle errors when multiple bioinformatics services fail?

Cross-database identifier mapping handles service failures using robust error handling with clear fallbacks. This ensures automated mapping pipelines continue operating reliably when querying services like UniProt, KEGG, or ChEMBL during batch processing.