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bioservices

Unify bioinformatics database queries and identifier mapping in Python workflows.

Updated Jul 1, 2026
Search Tags:#bioinformatics#pathway analysis#protein annotation#identifier mapping#blast#uniprot#kegg
One-click install
npx skills add https://github.com/jasrajtulsi/GRAD-SCOPE --skill bioservices-jasrajtulsi
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: bioservices
Source: https://github.com/jasrajtulsi/GRAD-SCOPE/tree/main/.claude/skills/bioservices
Command: npx skills add https://github.com/jasrajtulsi/GRAD-SCOPE --skill bioservices-jasrajtulsi

SYSTEM DOCUMENTATION & REQUIREMENTS

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

What problem does it solve?

This Skill removes the friction of jumping between separate bioinformatics services by unifying protein, pathway, compound, interaction, and annotation lookups into one workflow.

Core Features & Use Cases

  • Protein analysis: Search UniProt entries, retrieve FASTA sequences, map identifiers, and discover related KEGG pathways.
  • Batch identifier conversion: Convert many IDs at once between UniProt, KEGG, Ensembl, RefSeq, HGNC, and related databases with chunking and retry logic.
  • Compound cross-referencing: Resolve a compound name across KEGG, ChEBI, and ChEMBL to compare identifiers and basic properties.
  • Network and function context: Pull PSICQUIC interaction data and QuickGO annotations to support pathway and function analysis.
  • Use case: Analyze a protein such as ZAP70, then return its UniProt accession, sequence, pathways, interaction partners, and GO terms in one coordinated result.

Quick Start

Ask for a bioinformatics lookup on a protein or compound and include the databases you want connected, such as UniProt, KEGG, ChEBI, ChEMBL, PSICQUIC, or QuickGO.

Frequently Asked Questions about bioservices

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

FAQPage Schema
How do I query multiple bioinformatics databases like UniProt and KEGG in one workflow?▼

You can query bioinformatics databases together by using a unified Python workflow that retrieves protein entries, FASTA sequences, and KEGG pathways in a single coordinated request. This eliminates the friction of jumping between separate services.

Can I batch convert protein identifiers between UniProt, Ensembl, and RefSeq?▼

Yes, batch identifier conversion is supported for UniProt, KEGG, Ensembl, RefSeq, and HGNC databases. The workflow includes chunking and retry logic to process many IDs at once and reliably map them between databases.

Does this bioinformatics workflow require a specific Python environment or internet access?▼

This bioinformatics workflow requires internet access and Python 3.9 through 3.12. For NCBI BLAST submissions, optional email handling is needed to manage queries and retrieve sequence-analysis results.

What is the best way to retrieve protein interaction partners and GO terms for pathway analysis?▼

The best way to retrieve protein interaction partners and GO terms is to pull PSICQUIC interaction data and QuickGO annotations. This provides network and functional context to support comprehensive pathway analysis.

How do I cross-reference chemical compounds across KEGG, ChEBI, and ChEMBL?▼

Compound cross-referencing resolves a chemical name across KEGG, ChEBI, and ChEMBL databases. This allows you to compare compound identifiers and basic properties within a single bioinformatics workflow.

Can I run NCBI BLAST searches and retrieve sequences alongside UniProt lookups?▼

Yes, NCBI BLAST searches are supported for sequence-analysis retrieval alongside UniProt lookups. The workflow unifies protein, pathway, and annotation tasks, requiring internet access and optional NCBI email handling for BLAST submissions.

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