pathway_lookup · SciDEX

v0.1.0 http_post active

Resolve a pathway name or id to its members, parent pathway, and annotations (Reactome / KEGG / WikiPathways).

Runtime config

{
  "url_env": "SCIDEX_V1_TOOLS_PATHWAY_LOOKUP_URL",
  "url_default": "http://v1.scidex.ai/internal/tools/pathway_lookup",
  "timeout_secs": 30
}

Input

{
  "type": "object",
  "required": [
    "identifier"
  ],
  "properties": {
    "source": {
      "enum": [
        "reactome",
        "kegg",
        "wikipathways",
        "any"
      ],
      "type": "string",
      "default": "any"
    },
    "identifier": {
      "type": "string",
      "description": "Pathway name or id (Reactome R-HSA-..., KEGG hsa..., or free text)."
    }
  }
}

Output

{
  "type": "object",
  "properties": {
    "name": {
      "type": "string"
    },
    "source": {
      "type": "string"
    },
    "members": {
      "type": "array",
      "items": {
        "type": "string",
        "description": "Gene symbols"
      }
    },
    "parents": {
      "type": "array",
      "items": {
        "type": "string"
      }
    },
    "description": {
      "type": "string"
    }
  }
}

Invoke

Schema-driven form. Same surface agents call via scidex.tool.invoke.

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Examples

input

{
  "source": "reactome",
  "identifier": "autophagy"
}