`rgd_rat` read

scidex.forge.rgd_rat

Query the Rat Genome Database (RGD) for rat gene data including disease annotations and pathway associations. For each gene symbol, returns the RGD accession ID, rat symbol, full name, chromosome, gene type, human ortholog, disease associations (RDO/OMIM terms with evidence codes), and pathway annotations from KEGG and Reactome. Human gene symbols (e.g. TP53) are automatically resolved to their rat ortholog via RGD search. Up to 10 symbols per call; up to 5 concurrent gene lookups. Not-found symbols go to the not_found list — not an exception. Complements forge_mgi_mouse_gene (mouse) with rat-specific genomic and disease data. API: rest.rgd.mcw.edu/rgdws — public, no auth required.

HTTP: POST /api/scidex/forge/rgd_rat

Invoke

Calls scidex.tool.invoke on the substrate with this tool name. Edit the JSON below — it must match the input schema. The substrate runs the tool, records the call in substrate_tool_calls, and returns a structured envelope.

Schemas

Input schema

{
  "additionalProperties": false,
  "description": "Input schema for ``scidex.forge.rgd_rat``.",
  "properties": {
    "gene_symbols": {
      "description": "Rat gene symbols to look up (e.g. ['Trp53', 'Brca2']). Human gene symbols (all-uppercase, e.g. 'TP53') are resolved to their rat ortholog via RGD search. Maximum 10 symbols per call.",
      "items": {
        "type": "string"
      },
      "maxItems": 10,
      "minItems": 1,
      "title": "Gene Symbols",
      "type": "array"
    },
    "include_diseases": {
      "default": true,
      "description": "If True (default), include disease annotations from RGD. Set False to reduce response size.",
      "title": "Include Diseases",
      "type": "boolean"
    },
    "include_pathways": {
      "default": true,
      "description": "If True (default), include pathway annotations from RGD. Set False to reduce response size.",
      "title": "Include Pathways",
      "type": "boolean"
    }
  },
  "required": [
    "gene_symbols"
  ],
  "title": "ForgeRGDRatIn",
  "type": "object"
}

Output schema

{
  "$defs": {
    "RGDDiseaseAnnotation": {
      "description": "One disease annotation from RGD for a rat gene.",
      "properties": {
        "term_acc": {
          "description": "Ontology term accession (e.g. 'RDO:0005500', 'OMIM:151623').",
          "title": "Term Acc",
          "type": "string"
        },
        "term": {
          "description": "Disease term name.",
          "title": "Term",
          "type": "string"
        },
        "evidence_codes": {
          "description": "Evidence codes supporting the annotation (e.g. ['IMP', 'IEA']).",
          "items": {
            "type": "string"
          },
          "title": "Evidence Codes",
          "type": "array"
        },
        "data_src": {
          "default": "",
          "description": "Data source (e.g. 'RGD', 'OMIM').",
          "title": "Data Src",
          "type": "string"
        }
      },
      "required": [
        "term_acc",
        "term"
      ],
      "title": "RGDDiseaseAnnotation",
      "type": "object"
    },
    "RGDGeneResult": {
      "description": "One gene record from RGD.",
      "properties": {
        "rgd_id": {
          "description": "RGD accession ID (numeric).",
          "title": "Rgd Id",
          "type": "integer"
        },
        "symbol": {
          "description": "Rat gene symbol (e.g. 'Trp53').",
          "title": "Symbol",
          "type": "string"
        },
        "name": {
          "default": "",
          "description": "Full gene name/description.",
          "title": "Name",
          "type": "string"
        },
        "gene_type": {
          "default": "",
          "description": "Gene type (e.g. 'protein-coding', 'pseudo').",
          "title": "Gene Type",
          "type": "string"
        },
        "chromosome": {
          "default": "",
          "description": "Chromosome (e.g. '10', 'X').",
          "title": "Chromosome",
          "type": "string"
        },
        "human_ortholog": {
          "anyOf": [
            {
              "type": "string"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "Human gene symbol ortholog (e.g. 'TP53'), if known.",
          "title": "Human Ortholog"
        },
        "disease_annotations": {
          "description": "Disease associations curated by RGD.",
          "items": {
            "$ref": "#/$defs/RGDDiseaseAnnotation"
          },
          "title": "Disease Annotations",
          "type": "array"
        },
        "pathway_annotations": {
          "description": "Pathway annotations from KEGG, Reactome, and other sources.",
          "items": {
            "$ref": "#/$defs/RGDPathwayAnnotation"
          },
          "title": "Pathway Annotations",
          "type": "array"
        }
      },
      "required": [
        "rgd_id",
        "symbol"
      ],
      "title": "RGDGeneResult",
      "type": "object"
    },
    "RGDPathwayAnnotation": {
      "description": "One pathway annotation from RGD for a rat gene.",
      "properties": {
        "pathway_id": {
          "description": "Pathway ID (e.g. 'KEGG:rno05200', 'PANTHER:P00059').",
          "title": "Pathway Id",
          "type": "string"
        },
        "pathway_name": {
          "description": "Pathway name.",
          "title": "Pathway Name",
          "type": "string"
        },
        "data_src": {
          "default": "",
          "description": "Pathway database source.",
          "title": "Data Src",
          "type": "string"
        }
      },
      "required": [
        "pathway_id",
        "pathway_name"
      ],
      "title": "RGDPathwayAnnotation",
      "type": "object"
    }
  },
  "description": "Response shape for ``scidex.forge.rgd_rat``.",
  "properties": {
    "genes": {
      "description": "Gene records for found symbols.",
      "items": {
        "$ref": "#/$defs/RGDGeneResult"
      },
      "title": "Genes",
      "type": "array"
    },
    "not_found": {
      "description": "Input symbols that could not be resolved in RGD.",
      "items": {
        "type": "string"
      },
      "title": "Not Found",
      "type": "array"
    },
    "took_ms": {
      "description": "Wall-clock time for all upstream API calls.",
      "title": "Took Ms",
      "type": "integer"
    }
  },
  "required": [
    "took_ms"
  ],
  "title": "ForgeRGDRatOut",
  "type": "object"
}

curl snippet

Replace $SCIDEX_JWT with a valid bearer token. Read verbs are usually accessible without auth in dev; production requires a JWT.

curl -sS -X POST '/api/scidex/forge/rgd_rat' \
  -H 'authorization: Bearer $SCIDEX_JWT' \
  -H 'content-type: application/json' \
  -d '{
  "gene_symbols": []
}'

About this tool

rgd_rat is one of the substrate's Forge verbs — agent-callable wrappers around external biology and literature databases. Source of truth is the substrate's scidex.verbs introspection endpoint; this page is a thin browsable face on it.

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tokens

for agents scidex.tool.invoke

Invoke this Forge tool via scidex.tool.invoke. Returns a structured envelope with job_id, status, duration_ms, result, and error. Requires authentication. Check the schemas section for input/output contract.

POST /api/scidex/rpc
{
  "verb": "scidex.tool.invoke",
  "args": {
    "tool": "scidex.forge.rgd_rat",
    "args": {}
  }
}

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