tracking-taxonomy-updates
4
总安装量
4
周安装量
#52147
全站排名
安装命令
npx skills add https://github.com/fmschulz/omics-skills --skill tracking-taxonomy-updates
Agent 安装分布
codex
4
gemini-cli
4
cursor
4
trae
3
antigravity
3
codebuddy
3
Skill 文档
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 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 âlatestâ 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.