Gene Expression SPARQL SELECT (Bgee)

bgeesparql/sparql-select

Runs one read-only SPARQL SELECT over the Bgee knowledge graph (gene expression calls, genes, species, anatomical entities and orthology from the SIB Swiss Institute of Bioinformatics) and returns the SPARQL JSON results. The outer query is capped at `limit` rows (default 100, at most 500); write no PREFIX lines and no # comments, so write every IRI in full in angle brackets. The graph holds billions of triples: filter early, and expect a heavy aggregate to time out. Bgee data, passed through unmodified and served by Eden Engine; not an official Bgee 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

Bgee

Data from Bgee, the gene expression database of the SIB Swiss Institute of Bioinformatics (bgee.org), passed through unmodified. Credit: Bgee, SIB Swiss Institute of Bioinformatics. Served by Eden Engine; not an official Bgee or SIB 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: "bgeesparql/sparql-select" })

// 3. learn: read the usage guide at runtime
omnial_learn({ tool: "bgeesparql/sparql-select" })

// 4. run: price the exact call first, then run it
omnial_execute({ tool: "bgeesparql/sparql-select", input: { /* see input_schema */ }, dry_run: true })
omnial_execute({ tool: "bgeesparql/sparql-select", 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 24, 2026

Input and output schemas

Input schema

input_schema.json

{
  "type": "object",
  "required": [
    "query"
  ],
  "properties": {
    "limit": {
      "type": "integer",
      "default": 100,
      "maximum": 500,
      "minimum": 1,
      "description": "Most rows to return, 1 to 500. Default 100."
    },
    "query": {
      "type": "string",
      "pattern": "^(?![\\s\\S]*\\b[Ss][Ee][Rr][Vv][Ii][Cc][Ee]\\b)\\s*[Ss][Ee][Ll][Ee][Cc][Tt]\\b(?:[^#<]|<[^<>\\s]*>|<(?=[\\s=]))*$",
      "maxLength": 3000,
      "minLength": 8,
      "description": "One SPARQL SELECT over the Bgee knowledge graph, for example SELECT ?gene ?id WHERE { ?gene a <http://purl.org/net/orth#Gene> ; <http://purl.org/dc/terms/identifier> ?id }. Write every IRI in full, no PREFIX lines, no # comments and no SERVICE clause. Put no LIMIT on the outer query: the tool adds one from `limit`."
    }
  },
  "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, literal, typed-literal or bnode."
                },
                "value": {
                  "type": "string"
                },
                "datatype": {
                  "type": "string"
                },
                "xml:lang": {
                  "type": "string"
                }
              },
              "additionalProperties": true
            }
          },
          "description": "One object per result row, keyed by column name; each cell has `type` and `value` (plus `datatype` or `xml:lang` where they apply)."
        }
      },
      "additionalProperties": true
    }
  },
  "additionalProperties": true
}