scAgent/tools/validate_annotation.json at main · deepmind11/scAgent · GitHub

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{
  "name": "validate_annotation",
  "description": "Validate a cluster's cell type label by comparing its top DE markers against known marker databases. Returns confidence (high/medium/low), overlap ratio, matched markers, and alternative cell type suggestions.",
  "parameters": {
    "type": "object",
    "properties": {
      "cluster_markers": {
        "type": "array",
        "items": { "type": "string" },
        "description": "Top DE genes for the cluster (from rank_genes_groups or similar)."
      },
      "label": {
        "type": "string",
        "description": "Proposed cell type label to validate, e.g. 'NK cells'."
      },
      "species": {
        "type": "string",
        "enum": ["human", "mouse"],
        "default": "human",
        "description": "Species."
      },
      "top_n": {
        "type": "integer",
        "default": 20,
        "minimum": 5,
        "maximum": 50,
        "description": "How many known markers to compare against."
      }
    },
    "required": ["cluster_markers", "label"]
  },
  "returns": {
    "type": "object",
    "description": "Object with label, confidence (high/medium/low), overlap_ratio, matched_markers, total_known, evidence, alternatives."
  },
  "category": "knowledge",
  "callable": "scagent.tools.knowledge_tools.validate_annotation"
}