WikiPathways Pathways Containing a Gene Symbol

wikipathwayssparql/pathways-by-gene

Lists the WikiPathways pathways of one organism that contain a data node labelled with an exact gene symbol (case sensitive, for example TP53 for human or Trp53 for mouse) and returns one row per pathway with its WikiPathways IRI and title, sorted by title, up to `limit` rows (default 25, at most 100). Organism defaults to Homo sapiens. WikiPathways content (CC0) is passed through unmodified and served by Eden Engine; not an official WikiPathways product.

activeper callv1

Price

$0.0026 per call

You pay the price shown. If a call turns out to cost more than its quote, you pay the actual price, capped at twice the quote. No monthly minimum. Top-ups start at $0.50.

Data source

WikiPathways

Data from WikiPathways (https://www.wikipathways.org), released under a CC0 waiver. Served by Eden Engine; not an official WikiPathways product.

Use it

Five steps: search, inspect, learn, run, settle. No per-tool setup; your agent reaches this tool through the meta-tools it already has.

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agent

// 1. search: find the tool
omnial_search({ query: "what you need" })

// 2. inspect: price and input schema
omnial_inspect({ tool: "wikipathwayssparql/pathways-by-gene" })

// 3. learn: read the usage guide at runtime
omnial_learn({ tool: "wikipathwayssparql/pathways-by-gene" })

// 4. run: price the exact call first, then run it
omnial_execute({ tool: "wikipathwayssparql/pathways-by-gene", input: { /* see input_schema */ }, dry_run: true })
omnial_execute({ tool: "wikipathwayssparql/pathways-by-gene", input: { /* ... */ } })

// 5. settle: the call is charged when it finishes, nothing to do

Not connected yet? Point your MCP client at https://mcp.eden-engine.com/mcp, then copy a config for your client.

Pricing

Every charge this tool can incur.

Charge	Price
Per call	$0.0026

Updated: Oct 25, 2026

Input and output schemas

Input schema

input_schema.json

{
  "type": "object",
  "required": [
    "symbol"
  ],
  "properties": {
    "limit": {
      "type": "integer",
      "default": 25,
      "maximum": 100,
      "minimum": 1,
      "description": "Most rows to return, 1 to 100. Default 25."
    },
    "symbol": {
      "type": "string",
      "pattern": "^[A-Za-z0-9._-]+$",
      "maxLength": 40,
      "minLength": 1,
      "description": "Exact gene symbol as WikiPathways labels the node, for example TP53. Case sensitive."
    },
    "organism": {
      "enum": [
        "Homo sapiens",
        "Mus musculus",
        "Rattus norvegicus",
        "Bos taurus",
        "Saccharomyces cerevisiae",
        "Caenorhabditis elegans",
        "Danio rerio",
        "Drosophila melanogaster",
        "Arabidopsis thaliana",
        "Gallus gallus",
        "Canis familiaris",
        "Pan troglodytes"
      ],
      "type": "string",
      "default": "Homo sapiens",
      "description": "Organism the pathways belong to. Default Homo sapiens."
    }
  },
  "additionalProperties": false
}

Output schema

output_schema.json

{
  "type": "object",
  "required": [
    "head",
    "results"
  ],
  "properties": {
    "head": {
      "type": "object",
      "properties": {
        "vars": {
          "type": "array",
          "items": {
            "type": "string"
          },
          "description": "The names of the result columns."
        }
      },
      "additionalProperties": true
    },
    "results": {
      "type": "object",
      "required": [
        "bindings"
      ],
      "properties": {
        "bindings": {
          "type": "array",
          "items": {
            "type": "object",
            "additionalProperties": {
              "type": "object",
              "properties": {
                "type": {
                  "type": "string",
                  "description": "uri or literal."
                },
                "value": {
                  "type": "string"
                },
                "datatype": {
                  "type": "string"
                },
                "xml:lang": {
                  "type": "string"
                }
              },
              "additionalProperties": true
            }
          },
          "description": "One object per row, keyed by column name; each cell has `type` and `value` (plus `xml:lang` or `datatype` where they apply)."
        }
      },
      "additionalProperties": true
    }
  },
  "description": "SPARQL 1.1 JSON results, passed through unchanged.",
  "additionalProperties": true
}