Tracking Taxonomy Updates

Use authoritative sources to report taxonomy changes with explicit versions, dates, and provenance.

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

Task	Action
Sources	See reference/sources.md
Tools	See reference/tools.md
IDs/ranks	See reference/ranks-and-identifiers.md
Report template	See reference/report-template.md
QA checklist	See reference/qa-checklist.md
Environment	See 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

Issue: Conflicting taxonomy between sources
Solution: Report both with explicit conflict flags and provenance.

Issue: Missing stable IDs
Solution: Resolve via TaxonKit and capture merged/deleted taxid warnings.