tracking-taxonomy-updates
Original：🇺🇸 English
Translated
Track and reconcile taxonomy updates across NCBI, GTDB, ICTV, and community eukaryote frameworks with versioned provenance.
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Sourcefmschulz/omics-skills
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npx skill4agent add fmschulz/omics-skills tracking-taxonomy-updatesTags
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View Translation Comparison →Tracking Taxonomy Updates
Use authoritative sources to report taxonomy changes with explicit versions, dates, and provenance.
Instructions
- Determine scope (domain, timeframe, output type).
- Pull authoritative updates and release notes.
- Extract versioned changes and impacts.
- If assigning taxonomy, run domain-appropriate tools and normalize IDs.
- Deliver a versioned report with conflicts flagged.
Quick Reference
| Task | Action |
|---|---|
| Sources | See |
| Tools | See |
| IDs/ranks | See |
| Report template | See |
| QA checklist | See |
| Environment | See |
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
text
Domains: Bacteria + Archaea
Timeframe: last 12 months
Output: summary table + pipeline impact notesTroubleshooting
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.