Resolve ambiguous organism names to NCBI taxonomy IDs and fetch ENA genomic data.
npx skills add https://github.com/dannon/taxonomy-resolver --skill taxonomy-resolver
Please help me install this Agent Skill. Skill: taxonomy-resolver Source: https://github.com/dannon/taxonomy-resolver/tree/main/. Command: npx skills add https://github.com/dannon/taxonomy-resolver --skill taxonomy-resolver
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.
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.
High-intent search queries and answers about installing and using this skill.
Organism name resolution converts common or ambiguous names like 'E. coli' or 'house mouse' into precise NCBI taxonomy IDs. The Skill handles spelling variations and strains through the NCBI Taxonomy API, returning standardized scientific names and their corresponding taxonomy identifiers for accurate genomic database searches.
Yes. After resolving an organism's taxonomy ID, the Skill queries the ENA API to retrieve FASTQ files, genome assemblies, and other genomic data with technical specifications like sequencing platform, read length, and paired-end status, enabling you to identify suitable datasets for analysis.
The Skill recommends Intergalactic Workflow Commission (IWC) Galaxy workflows by matching workflow requirements to your organism, data type, and research intent. It performs compatibility checks between your ENA datasets and available analysis pipelines, such as transcriptomics workflows for RNA-seq data.
Yes. The Skill handles disambiguation of common names, spelling variations, and strain information through conversational input and NCBI Taxonomy API validation, resolving ambiguity to species-level precision so you get the correct organism identifier on the first attempt.
The Skill requires network access to api.ncbi.nlm.nih.gov for taxonomy validation and www.ebi.ac.uk for ENA data retrieval. It uses Python scripts to return structured results, so a stable internet connection and access to these external APIs are prerequisites.
The Skill resolves organism names one at a time through the NCBI Taxonomy API and retrieves associated ENA data for each resolved organism. For large-scale organism searches, you would run multiple resolutions sequentially using the resolve_taxonomy.py and search_ena.py scripts.
AvaTar-ArTsRetrieve biological sequences from NCBI and ENA into FASTA or GenBank formats.
MubasherMohammedDiscover and execute Galaxy bioinformatics tools via the BioBlend API.
jaechang-hitsParse FASTA, GenBank, and PDB files with Biopython for sequence analysis.
Teng-bioRetrieve and analyze biological sequences from NCBI and ENA databases.
