bioservices

Retrieve and integrate protein, pathway, compound, and GO annotation data via BioServices.

21|2|Updated Dec 8, 2025

Search Tags:#python #bioinformatics #identifier mapping #protein interactions #unichem #kegg pathways #quickgo

Ready to run

npx skills add https://github.com/silverstein/claude-scientific-skills-desktop --skill bioservices-silverstein

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: bioservices
Source: https://github.com/silverstein/claude-scientific-skills-desktop/tree/main/corpus/bioservices
Command: npx skills add https://github.com/silverstein/claude-scientific-skills-desktop --skill bioservices-silverstein

SYSTEM DOCUMENTATION & REQUIREMENTS

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

What problem does it solve?

This Skill removes the friction of stitching together multiple bioinformatics data sources by giving you a single Python interface for querying proteins, pathways, compounds, and gene ontology annotations.

Core Features & Use Cases

Unified access to 40+ bioinformatics services: Query and retrieve biological data across common databases like UniProt, KEGG, ChEMBL, PubChem, Reactome, and QuickGO.
Cross-database identifier mapping: Convert identifiers between protein/gene databases (e.g., UniProt ↔ KEGG/Ensembl/RefSeq) and compound databases (e.g., KEGG ↔ ChEMBL via UniChem).
Workflow-ready sequence and network analysis: Retrieve sequences, run BLAST, analyze KEGG pathways, and extract protein-protein interactions via PSICQUIC.

Quick Start

Ask the AI to show you a small Python workflow that maps a UniProt accession to KEGG pathways and then fetches GO annotations for the same UniProt protein.

Frequently Asked Questions about bioservices

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

FAQPage Schema

How do I map identifiers between UniProt and KEGG pathways in Python?▼

Identifier mapping between UniProt and KEGG in Python is done by querying a unified bioinformatics web service client that translates accessions across databases and returns structured pathway results.

What is the best way to query multiple bioinformatics databases like UniProt and ChEMBL together?▼

The best way to query multiple bioinformatics databases together is through a unified Python interface that standardizes REST and SOAP requests across services like UniProt and ChEMBL into consistent structured outputs.

Can I retrieve protein-protein interactions and GO annotations using a single Python script?▼

You can retrieve protein-protein interactions and GO annotations in a single Python script by orchestrating PSICQUIC for network querying and QuickGO for annotation retrieval through a unified bioinformatics client.

Does this Python bioinformatics client support BLAST similarity searches and sequence retrieval?▼

This Python bioinformatics client supports BLAST similarity searches and sequence retrieval by initializing the appropriate service methods and returning results in usable text formats or structured Python objects.

How do I parse KEGG pathway data and convert compound identifiers via UniChem?▼

Parsing KEGG pathway data and converting compound identifiers via UniChem involves using a Python bioinformatics service to orchestrate REST-backed retrieval, parse pathway outputs, and systematically map compounds across databases.

What limitations exist when stitching together REST and SOAP bioinformatics web services in Python?▼

Stitching together REST and SOAP bioinformatics web services in Python is limited by external service availability and the necessity to handle varied, database-specific response structures within your workflow.