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LeonChaoX
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bioservices

Query biological data across bioinformatics web services with unified Python APIs.

783|65|Updated Feb 27, 2026
Search Tags:#bioinformatics#api integration#pathway analysis#identifier mapping#gene ontology#protein sequence#compound cross-referencing
One-click install
npx skills add https://github.com/LeonChaoX/qinyan-academic-skills --skill bioservices-leonchaox
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: bioservices
Source: https://github.com/LeonChaoX/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/LeonChaoX/qinyan-academic-skills --skill bioservices-leonchaox

SYSTEM DOCUMENTATION & REQUIREMENTS

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

What problem does it solve?

BioServices eliminates fragmented, database-specific code by providing a single unified Python interface for querying and integrating data across many bioinformatics web services.

Core Features & Use Cases

  • Unified multi-database querying: Retrieve protein, pathway, compound, GO, and interaction data through consistent Python calls.
  • Cross-database ID mapping: Convert identifiers across services (e.g., UniProt ↔ KEGG; KEGG/ChEBI/ChEMBL linkages via UniChem patterns).
  • Sequence and network workflows: Run sequence similarity searches (e.g., BLAST via BioServices) and extract pathway interaction networks (e.g., KEGG KGML to SIF/relations).
  • Use Case: Given a list of UniProt accessions for a target study, map them to KEGG genes, pull relevant pathways, then retrieve interaction partners and GO annotations to build an integrated analysis dataset.

Quick Start

Use the bioservices skill to map a UniProt accession to KEGG IDs and then fetch KEGG pathway IDs associated with that gene in a single Python workflow.

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 in Python?▼

You can map UniProt identifiers to KEGG pathways by using a unified Python API to perform cross-database queries, pulling relevant pathway IDs and extracting interaction networks via KGML parsing.

What's the best way to query multiple bioinformatics databases without writing database-specific code?▼

Querying multiple bioinformatics databases without database-specific code is achieved through a unified Python interface that supports REST and SOAP/WSDL backends to retrieve proteins, pathways, and compounds consistently.

Can I perform batch identifier mapping across ChEBI and ChEMBL?▼

Yes, you can perform batch identifier mapping and compound cross-referencing across ChEBI and ChEMBL by leveraging service integrations and UniChem patterns within a single Python workflow.

How does cross-database identifier mapping work for gene ontology annotations?▼

Cross-database identifier mapping for gene ontology annotations works by unifying bioinformatics service calls to retrieve biological data, enabling downstream parsing to extract GO terms for target sequences.

Does this bioinformatics API integration support sequence similarity searches and interaction network extraction?▼

Yes, this bioinformatics API integration supports sequence similarity searches like BLAST and enables extracting pathway interaction networks by converting KEGG KGML data into SIF and relations formats.

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