taxonomy-resolver

What problem does it solve?

This Skill eliminates the complexity of identifying organisms, searching vast genomic databases, and finding appropriate analysis workflows. It automates the resolution of ambiguous names, retrieves precise data, and recommends vetted analysis pipelines, saving researchers significant time and ensuring accuracy in their bioinformatics tasks.

Core Features & Use Cases

• Organism Name Resolution: Converts common or ambiguous names (e.g., "malaria parasite", "E. coli", "house mouse") into precise scientific names and NCBI taxonomy IDs, handling disambiguation through natural conversation.
• Genomic Data Search: Finds FASTQ files, genome assemblies, and other genomic data in the European Nucleotide Archive (ENA), providing crucial technical specifications (e.g., sequencing platform, read length, paired-end status).
• IWC Workflow Recommendation: Recommends relevant Intergalactic Workflow Commission (IWC) Galaxy workflows for bioinformatics analysis, intelligently matching workflow requirements to your specific data characteristics and research intent.
• Use Case: A researcher needs to analyze RNA-seq data for a specific Plasmodium falciparum strain. This Skill can resolve the organism, find available RNA-seq FASTQ datasets in ENA with their technical details, and then recommend suitable "Transcriptomics" workflows from the IWC Galaxy catalog, complete with compatibility checks for the data.

Quick Start

Ask Claude: "What's the taxonomy ID for house mouse?" Claude will use the skill to provide the precise NCBI taxonomy ID for Mus musculus.