Forge Tools rgd_quantitative_traits

rgd_quantitative_traits read

scidex.forge.rgd_quantitative_traits

Query the Rat Genome Database (RGD) for quantitative trait loci (QTL) data. Returns QTL records with chromosomal positions, LOD scores, p-values, trait/phenotype associations, and candidate gene lists. Covers cardiovascular, metabolic, neurological, behavioural, and other rat phenotypes. Complements gene-level RGD data with QTL-level genomic trait mapping for translational research. API: https://rest.rgd.mcw.edu/rgdws/ — public, no authentication required.

HTTP: POST /api/scidex/forge/rgd_quantitative_traits

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.

Sign in to invoke this tool. Schema and curl snippet are visible to anyone.

Schemas

Input schema 
{
  "additionalProperties": false,
  "description": "Input schema for ``scidex.forge.rgd_quantitative_traits``.",
  "properties": {
    "phenotype_term": {
      "description": "Phenotype or trait keyword to search (e.g. ``blood pressure``, ``body weight``, ``glucose tolerance``, ``anxiety``, ``bone density``). Matched against RGD QTL trait names and descriptions.",
      "maxLength": 200,
      "minLength": 1,
      "title": "Phenotype Term",
      "type": "string"
    },
    "chromosome": {
      "default": "",
      "description": "Chromosome filter (e.g. ``1``, ``4``, ``X``). When empty, returns QTLs from all chromosomes.",
      "maxLength": 5,
      "title": "Chromosome",
      "type": "string"
    },
    "species": {
      "default": "rat",
      "description": "Species to query: ``rat`` (default), ``mouse``, or ``human``. RGD primarily covers rat genetics but also curates mouse and human QTL data.",
      "title": "Species",
      "type": "string"
    },
    "limit": {
      "default": 20,
      "description": "Maximum number of QTL records to return. Default 20.",
      "maximum": 100,
      "minimum": 1,
      "title": "Limit",
      "type": "integer"
    }
  },
  "required": [
    "phenotype_term"
  ],
  "title": "ForgeRGDQTLIn",
  "type": "object"
}
Output schema 
{
  "$defs": {
    "RGDQTLRecord": {
      "description": "One RGD quantitative trait locus record.",
      "properties": {
        "qtl_rgd_id": {
          "description": "RGD numeric ID for the QTL.",
          "title": "Qtl Rgd Id",
          "type": "string"
        },
        "symbol": {
          "default": "",
          "description": "QTL symbol (e.g. ``Bp1``, ``Bmd1``).",
          "title": "Symbol",
          "type": "string"
        },
        "name": {
          "default": "",
          "description": "Full QTL name.",
          "title": "Name",
          "type": "string"
        },
        "chromosome": {
          "default": "",
          "description": "Chromosome (e.g. ``1``, ``X``).",
          "title": "Chromosome",
          "type": "string"
        },
        "start_pos": {
          "default": 0,
          "description": "Genomic start position (bp).",
          "title": "Start Pos",
          "type": "integer"
        },
        "stop_pos": {
          "default": 0,
          "description": "Genomic stop position (bp).",
          "title": "Stop Pos",
          "type": "integer"
        },
        "lod_score": {
          "anyOf": [
            {
              "type": "number"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "Maximum LOD score (higher values indicate stronger QTL evidence).",
          "title": "Lod Score"
        },
        "p_value": {
          "anyOf": [
            {
              "type": "number"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "Statistical significance p-value for this QTL.",
          "title": "P Value"
        },
        "species": {
          "default": "rat",
          "description": "Species (e.g. ``rat``).",
          "title": "Species",
          "type": "string"
        },
        "trait_name": {
          "default": "",
          "description": "Phenotype or trait associated with this QTL.",
          "title": "Trait Name",
          "type": "string"
        },
        "associated_genes": {
          "description": "Candidate gene symbols in the QTL region (up to 10).",
          "items": {
            "type": "string"
          },
          "title": "Associated Genes",
          "type": "array"
        },
        "rgd_url": {
          "default": "",
          "description": "RGD portal URL for this QTL.",
          "title": "Rgd Url",
          "type": "string"
        }
      },
      "required": [
        "qtl_rgd_id"
      ],
      "title": "RGDQTLRecord",
      "type": "object"
    }
  },
  "description": "Response shape for ``scidex.forge.rgd_quantitative_traits``.",
  "properties": {
    "qtls": {
      "description": "RGD QTL records, capped at ``limit``.",
      "items": {
        "$ref": "#/$defs/RGDQTLRecord"
      },
      "title": "Qtls",
      "type": "array"
    },
    "total_found": {
      "default": 0,
      "description": "Total QTLs found before applying limit.",
      "title": "Total Found",
      "type": "integer"
    },
    "took_ms": {
      "default": 0,
      "description": "Wall-clock time for the upstream call.",
      "title": "Took Ms",
      "type": "integer"
    }
  },
  "title": "ForgeRGDQTLOut",
  "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_quantitative_traits' \
  -H 'authorization: Bearer $SCIDEX_JWT' \
  -H 'content-type: application/json' \
  -d '{
  "phenotype_term": ""
}'

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