Tracking Taxonomy Updates

Instructions

1. Determine scope (domain, timeframe, output type).
2. Pull authoritative updates and release notes.
3. Extract versioned changes and impacts.
4. If assigning taxonomy, run domain-appropriate tools and normalize IDs.
5. Deliver a versioned report with conflicts flagged.

Quick Reference

reference/sources.md

reference/tools.md

reference/ranks-and-identifiers.md

reference/report-template.md

reference/qa-checklist.md

env/README.md

Input Requirements

• Domain(s) and timeframe
• Source systems to compare (NCBI/GTDB/ICTV/etc.)
• Sequences or genomes (for assignment workflows)

Output

• Versioned taxonomy update summary
• Conflict report across sources
• Standardized taxonomy assignment table (when applicable)

Quality Gates

• Every “latest” claim includes date, version, and authority
• Stable identifiers used for joins (taxids, GTDB IDs)
• Provenance captured (tool version, DB release, run date)

Examples

Example 1: Update scan scope

Domains: Bacteria + Archaea
Timeframe: last 12 months
Output: summary table + pipeline impact notes

Troubleshooting