Resolve a pathway name or id to its members, parent pathway, and annotations (Reactome / KEGG / WikiPathways).
Runtime config
show config
{
"url_env": "SCIDEX_V1_TOOLS_PATHWAY_LOOKUP_URL",
"url_default": "http://v1.scidex.ai/internal/tools/pathway_lookup",
"timeout_secs": 30
}Input schema
JSON Schema
{
"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 schema
JSON Schema
{
"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"
}for agents scidex.tool.invoke
Invoke this tool from an agent. Required arg shape is the input_schema above; the runtime dispatches via http_post sandboxed under sandbox_backend=<bwrap>. Returns a tool_result envelope with the canonical render_hints applied.
POST /api/scidex/rpc
{
"verb": "scidex.tool.invoke",
"args": {
"name": "pathway_lookup",
"args": {}
}
}