Genomic Data Skills for Claude

This repository contains two complementary Claude skills for working with genomic data:

Skills

🧬 taxonomy-resolver

Purpose: Find and identify genomic data

Resolves organism names to NCBI taxonomy IDs, searches ENA for genomic data (FASTQ, assemblies), and retrieves BioProject details.

Key features:

• Convert common names to scientific names with disambiguation
• Search NCBI Taxonomy API for validation
• Find FASTQ files, assemblies, and other data in ENA
• Group results by BioProject with technical details
• Intent-based filtering (RNA-Seq, WGS, ChIP-Seq, etc.)

APIs used: NCBI Taxonomy, ENA (European Nucleotide Archive)

🔬 iwc-workflow-recommender

Purpose: Recommend Galaxy workflows for analysis

Searches the IWC (Intergalactic Workflow Commission) workflow catalog and recommends appropriate workflows for genomic analysis.

Key features:

• Search IWC workflow catalog by category
• Match workflows to organisms and data types
• Check data compatibility (single/paired-end, platform, etc.)
• Provide TRS IDs for importing into Galaxy
• ALWAYS recommends existing workflows (never writes custom code)

APIs used: IWC Workflow Manifest

Repository Structure

taxonomy-resolver/          (the repository)
├── taxonomy-resolver/      (skill: data discovery)
│   ├── resolve_taxonomy.py
│   ├── search_ena.py
│   ├── get_bioproject_details.py
│   ├── SKILL.md
│   ├── README.md
│   └── ...
├── iwc-workflow-recommender/  (skill: workflow recommendation)
│   ├── search_iwc_workflows.py
│   ├── SKILL.md
│   ├── README.md
│   └── ...
├── CLAUDE.md               (project-level guidance for Claude Code)
└── README.md               (this file)

Installation

For Claude Code

Copy both skill directories to your Claude skills folder:

cp -r taxonomy-resolver ~/.claude/skills/
cp -r iwc-workflow-recommender ~/.claude/skills/

For Claude.ai

Build each skill separately:

cd taxonomy-resolver && ./build.sh
cd ../iwc-workflow-recommender && ./build.sh

Then upload the generated ZIP files to Claude.ai (Settings → Features → Skills).

Testing

Each skill has its own test suite:

# Test taxonomy-resolver
cd taxonomy-resolver && bash test_skill.sh

# Test iwc-workflow-recommender
cd iwc-workflow-recommender && bash test_skill.sh

Network Requirements

Both skills require network access. Add these domains to your Claude environment's allowlist:

taxonomy-resolver:

• api.ncbi.nlm.nih.gov
• www.ebi.ac.uk

iwc-workflow-recommender:

• iwc.galaxyproject.org

Philosophy

Both skills follow the principle: "Let the APIs do the work, Claude just orchestrates."

• No data invention: Always defer to external APIs for authoritative information
• No code generation: The IWC workflow recommender strictly prohibits writing custom analysis scripts
• Disambiguation first: Never pass ambiguous inputs to APIs without clarification
• Focused responsibilities: Each skill has one clear purpose

Workflow Example

A typical user interaction might use both skills:

1. taxonomy-resolver: "Find RNA-seq data for Plasmodium falciparum"

   • Resolves organism name to taxonomy ID
   • Searches ENA with RNA-Seq filter
   • Returns BioProjects grouped by study with technical details

2. iwc-workflow-recommender: "What workflows can I use for this data?"

   • Searches IWC catalog for Transcriptomics workflows
   • Matches workflows to eukaryotic parasites
   • Checks compatibility with paired-end Illumina data
   • Recommends appropriate workflows with TRS IDs

License

Apache 2.0

Related Resources

• NCBI Taxonomy Database
• ENA (European Nucleotide Archive)
• IWC Workflow Catalog
• Galaxy Project
• Anthropic Skills Documentation