literature-taxonomy-curation

name	literature-taxonomy-curation
description	Use when an agent must define viral genotype, subtype, clade, lineage, target/background groups, or PhyloGuide groups from cited literature before primer or tNGS panel design.

Literature Taxonomy Curation

Use this skill before prepare-phylo or production primer design when group names affect the result. Do not infer genotype/subtype from sequence names alone.

Workflow

1. Identify the exact species/virus, host, region/date scope, and design purpose.
2. Search primary taxonomy/genotype papers, ICTV/NCBI/public-health references, and recent surveillance papers.
3. Extract group names, representative accessions, distance thresholds or clade criteria, and citations.
4. Write a taxonomy JSON with species, optional target_group, references, and groups.
5. Validate it:

python agentskill/scripts/curate_references.py validate-taxonomy \
  --taxonomy-json taxonomy.json \
  --output taxonomy_report.json

Optional PubMed search helper:

python agentskill/scripts/curate_references.py search-literature \
  --species "Target virus" \
  --extra-query "complete genome" \
  --max-records 20 \
  --output literature_candidates.json

Required Output

The downstream agent should receive:

• taxonomy.json: curated groups and references.
• taxonomy_report.json: validation status, warnings, and errors.
• A short rationale explaining why these groups are appropriate for the current species and use case.

If the species is missing or ambiguous, ask for clarification before assigning groups.