bioservices

Map identifiers across bioinformatics databases within Python workflows.

52|6|Updated Nov 24, 2025

Search Tags:#bioinformatics #KEGG #UniProt #bioservices #GO

Ready to run

npx skills add https://github.com/ovachiever/droid-tings --skill bioservices-ovachiever

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: bioservices
Source: https://github.com/ovachiever/droid-tings/tree/main/skills/bioservices
Command: npx skills add https://github.com/ovachiever/droid-tings --skill bioservices-ovachiever

SYSTEM DOCUMENTATION & REQUIREMENTS

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

What problem does it solve?

Unifies access to multiple bioinformatics databases and services, enabling cross-database queries, ID mappings, and workflow-driven data retrieval.

Core Features & Use Cases

Protein sequence retrieval, pathway discovery, and GO annotations
Cross-database identifier mappings (UniProt, KEGG, ChEBI, ChEMBL, PubChem)
Batch analyses and integrated workflow scripting
Supports REST and SOAP services across 40+ resources

Quick Start

Use UniProt to map a protein ID to KEGG and retrieve a pathway, then fetch GO annotations.

Frequently Asked Questions about bioservices

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

FAQPage Schema

How do I map protein IDs across multiple bioinformatics databases?▼

Protein ID mapping across databases like UniProt, KEGG, and ChEBI is unified through bioservices, which handles cross-database queries and returns structured outputs (dictionaries or CSV) for downstream analysis without managing each API separately.

Can I retrieve sequences and pathway data from UniProt and KEGG in a single Python workflow?▼

Yes. Bioservices integrates 40+ bioinformatics services including UniProt and KEGG, enabling batch retrieval of protein sequences, pathways, and GO annotations within one Python script with built-in chunking and error handling.

What's the best way to perform batch processing across REST and SOAP bioinformatics services?▼

Bioservices abstracts REST and SOAP protocol differences, supporting batch processing with chunking and error handling across UniProt, KEGG, ChEMBL, PubChem, and other resources, returning structured outputs for automation.

Do I need to write separate API clients for UniProt, KEGG, and GO annotations?▼

No. Bioservices provides unified access to UniProt, KEGG, ChEMBL, PubChem, GO, Reactome, BioGRID, and related resources through a single Python toolkit, eliminating duplicate API integration work.

How do I retrieve compound data and cross-reference identifiers from ChEMBL and PubChem together?▼

Bioservices enables querying ChEMBL and PubChem within the same workflow, handling identifier mapping and batch retrieval with structured output generation for integrated compound and protein data analysis.

What happens if a bioinformatics database query fails during batch processing?▼

Bioservices includes built-in error handling and chunking for batch operations, gracefully managing failures across REST and SOAP services so incomplete results don't halt the entire workflow.