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cultivarium-data

Query CVM strain data for genomes, screens, MIC, and annotations.

1|Updated Apr 29, 2026
Search Tags:#cvm#methylation#cultivarium#strain-dataset#genome-metadata#ori-screen#antibiotic-susceptibility
One-click install
npx skills add https://github.com/cultivarium/hermes-starter-kit --skill cultivarium-data
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: cultivarium-data
Source: https://github.com/cultivarium/hermes-starter-kit/tree/main/skills/cultivarium-data
Command: npx skills add https://github.com/cultivarium/hermes-starter-kit --skill cultivarium-data

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes references (resource) components.

What problem does it solve?

Look up Cultivarium's public CVM strain dataset — strain inventory, genome assembly metadata, ORI/plasmid screen results, growth/media screen data, MIC antibiotic susceptibility, methylation motifs and RM gene annotations, and ML-predicted phenotypes (optimal temperature, pH, salinity, oxygen tolerance). Use whenever the user asks about a CVM strain (e.g. CVM022, CVM086) or wants to filter Cultivarium's strain data — which ORIs work in a strain, what media a strain grows in, antibiotic resistance, methylation motifs, predicted growth conditions, ATCC/DSM/NCBI cross-references, or genome download links.

Core Features & Use Cases

  • Retrieve strain inventories, genome assembly metadata, ORI screen results, and growth/media data for CVM strains.
  • Cross-reference strains to public catalogs (ATCC, DSM, NCBI) and map identifiers across datasets.
  • Explore methylation motifs, RM gene annotations, and ML-predicted phenotypes (temperature, pH, salinity, oxygen tolerance) for a strain.

Quick Start

Ask it to fetch all available data for a specific CVM strain (e.g. CVM022), including genome, growth conditions, and MIC info.

Frequently Asked Questions about cultivarium-data

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

FAQPage Schema
How do I look up genome metadata and growth conditions for a specific CVM strain?▼

You can retrieve CVM strain data by querying the gzipped CSV datasets for a specific strain identifier. This returns genome assembly metadata, growth media screens, ML-predicted phenotypes, and antibiotic susceptibility information for that strain.

Can I cross-reference CVM strain identifiers with ATCC, DSM, or NCBI catalog numbers?▼

Yes, the strain inventory dataset enables cross-referencing CVM strain identifiers with ATCC, DSM, and NCBI catalog numbers. This allows you to map identifiers across public catalogs and locate corresponding genome download links.

What methylation motifs and restriction-modification gene annotations are available for bacterial genomes?▼

The CVM strain dataset includes methylation motifs and RM gene annotations for bacterial genomes. Querying the dataset provides specific methylation patterns and restriction-modification system gene annotations for each analyzed strain.

How do I find antibiotic susceptibility and MIC data for a bacterial strain?▼

To find antibiotic susceptibility and MIC data, query the CVM strain dataset minimum inhibitory concentration tables. This returns MIC values and antibiotic resistance profiles to identify which strains tolerate specific antibiotic treatments.

Does the dataset include ORI screen results to identify which plasmid origins of replication work in a strain?▼

Yes, the dataset includes ORI screen results to identify compatible plasmid origins of replication. Querying the ORI screen data reveals which origins of replication function within a specific CVM strain.

What are the limitations when cross-referencing strain data across different genome datasets?▼

A limitation when cross-referencing strain data is the dependency on shared identifier columns for accurate joins across the gzipped CSV datasets. Users must consult the reference documentation to correctly interpret column semantics and avoid mismatching strain records.

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