bioservices

Query bioinformatics databases and map identifiers through a unified Python interface.

Updated May 24, 2026
One-click install
npx skills add https://github.com/Estrella-231/Mathematical_modeling_tongmeng --skill bioservices-estrella-231
Or copy as Structured Prompt for Agent
Please help me install this Agent Skill.
Skill: bioservices
Source: https://github.com/Estrella-231/Mathematical_modeling_tongmeng/tree/main/.agents/skills/bioservices
Command: npx skills add https://github.com/Estrella-231/Mathematical_modeling_tongmeng --skill bioservices-estrella-231

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes references (resource) components.

What problem does it solve?

Bioinformatics workflows often stall when you need to query many biological databases and reconcile incompatible identifier formats; BioServices solves this by providing a unified Python interface for cross-database retrieval, mapping, and analysis.

Core Features & Use Cases

  • Cross-database identifier mapping: Convert protein/gene/compound identifiers across services like UniProt ↔ KEGG and KEGG → ChEMBL via UniChem.
  • Multi-service data retrieval: Fetch sequences, annotations, pathway data, interaction data, and gene ontology terms in a consistent workflow.
  • Workflow-ready integration: Compose end-to-end pipelines in Python (REST/SOAP handled transparently) for quick analysis and automation across biological resources.

Quick Start

Use the bioservices skill to map a list of UniProt accessions to KEGG gene IDs in one batch and export the results for downstream analysis.

Frequently Asked Questions about bioservices

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

FAQPage Schema
How do I map bioinformatics identifiers across UniProt and KEGG in Python?

Identifier mapping across UniProt and KEGG is achieved via a unified Python API that handles cross-database retrieval. You batch query protein or gene lists to reconcile incompatible formats into consistent target database IDs for downstream pipelines.

What is the best way to query multiple biological databases like ChEMBL and QuickGO in one workflow?

Querying multiple biological databases like ChEMBL and QuickGO in one workflow requires a unified Python interface that handles REST and SOAP/WSDL protocols transparently. This provides consistent method calls to search, retrieve, and parse multi-database results within a single pipeline.

Can I retrieve sequences and pathway data using a single Python API for bioinformatics?

Yes, you can retrieve sequences and pathway data using a single Python API for bioinformatics. It supports consistent method calls across services like UniProt and KEGG to fetch annotations and discover pathway memberships within one analysis pipeline.

Does this Python API handle rate-limited batch querying for large bioinformatics datasets?

Rate-limited batch querying for large bioinformatics datasets is supported natively by the API. It manages request pacing across services like NCBI BLAST and UniChem to prevent timeouts and ensure complete multi-database data aggregation.

How do I convert chemical compound identifiers across UniChem and ChEBI?

Converting chemical compound identifiers across UniChem and ChEBI is performed through cross-database identifier mapping. The API provides consistent method calls to translate compound accessions and export mapped results for downstream chemical analysis pipelines.