Forge Tools bgee

bgee read

scidex.forge.bgee

Query Bgee (bgee.org) for comparative gene expression data across 30+ animal species, integrating RNA-seq, Affymetrix, and EST/in situ experiments with Uberon anatomical ontology and developmental stage annotations. Enables ortholog-aware cross-species expression comparison. Distinct from scidex.forge.gtex_expression (human eQTL) and scidex.forge.cellxgene_expression (single-cell). Input: gene symbol or Ensembl ID, optional species (default 'Homo sapiens'), data_type (RNA_Seq|Affymetrix|EST|In_situ|FULL_LENGTH), limit. API: GET https://www.bgee.org/api/?page=gene&action=expression — free, no auth.

HTTP: POST /api/scidex/forge/bgee

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.bgee``.",
  "properties": {
    "gene": {
      "description": "Gene symbol or Ensembl gene ID to query (e.g. ``'TP53'``, ``'BRCA1'``, ``'ENSG00000141510'``). Passed directly to the Bgee gene_id parameter.",
      "maxLength": 100,
      "title": "Gene",
      "type": "string"
    },
    "species": {
      "default": "Homo sapiens",
      "description": "Scientific species name for the query. Defaults to ``'Homo sapiens'``. Supported values include: Mus musculus, Rattus norvegicus, Danio rerio, Drosophila melanogaster, Caenorhabditis elegans, and 10+ other animal species catalogued in Bgee.",
      "maxLength": 200,
      "title": "Species",
      "type": "string"
    },
    "data_type": {
      "default": "RNA_Seq",
      "description": "Expression data type to retrieve. Accepted values: ``'RNA_Seq'``, ``'Affymetrix'``, ``'EST'``, ``'In_situ'``, ``'FULL_LENGTH'``. Default ``'RNA_Seq'``.",
      "title": "Data Type",
      "type": "string"
    },
    "limit": {
      "default": 20,
      "description": "Maximum number of expression call records to return. Default 20.",
      "maximum": 500,
      "minimum": 1,
      "title": "Limit",
      "type": "integer"
    }
  },
  "required": [
    "gene"
  ],
  "title": "ForgeBgeeIn",
  "type": "object"
}
Output schema 
{
  "$defs": {
    "BgeeExpression": {
      "description": "One expression call record from Bgee.",
      "properties": {
        "anatomical_entity": {
          "description": "Anatomical structure / tissue name (from Uberon ontology).",
          "title": "Anatomical Entity",
          "type": "string"
        },
        "anatomical_entity_id": {
          "default": "",
          "description": "Uberon ontology identifier for the anatomical entity (e.g. 'UBERON:0001385').",
          "title": "Anatomical Entity Id",
          "type": "string"
        },
        "developmental_stage": {
          "default": "",
          "description": "Developmental stage label (e.g. 'post-juvenile adult stage').",
          "title": "Developmental Stage",
          "type": "string"
        },
        "expression_score": {
          "description": "Normalised expression score in [0.0, 1.0] (higher = more expressed).",
          "title": "Expression Score",
          "type": "number"
        },
        "call_type": {
          "description": "Expression call type: ``'EXPRESSED'`` or ``'NOT_EXPRESSED'``.",
          "title": "Call Type",
          "type": "string"
        },
        "species": {
          "default": "",
          "description": "Species name for this expression call.",
          "title": "Species",
          "type": "string"
        }
      },
      "required": [
        "anatomical_entity",
        "expression_score",
        "call_type"
      ],
      "title": "BgeeExpression",
      "type": "object"
    }
  },
  "description": "Response shape for ``scidex.forge.bgee``.",
  "properties": {
    "gene": {
      "description": "The gene symbol / ID that was queried.",
      "title": "Gene",
      "type": "string"
    },
    "species": {
      "description": "The species name that was queried.",
      "title": "Species",
      "type": "string"
    },
    "expressions": {
      "description": "Expression call records from Bgee, sorted by expression_score descending, capped at ``limit``.",
      "items": {
        "$ref": "#/$defs/BgeeExpression"
      },
      "title": "Expressions",
      "type": "array"
    },
    "not_found": {
      "default": false,
      "description": "True when Bgee returned no expression data for this gene/species combination.",
      "title": "Not Found",
      "type": "boolean"
    },
    "source": {
      "default": "Bgee (bgee.org)",
      "description": "Data source attribution.",
      "title": "Source",
      "type": "string"
    },
    "took_ms": {
      "default": 0,
      "description": "Wall-clock time for the upstream API call in milliseconds.",
      "title": "Took Ms",
      "type": "integer"
    }
  },
  "required": [
    "gene",
    "species"
  ],
  "title": "ForgeBgeeOut",
  "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/bgee' \
  -H 'authorization: Bearer $SCIDEX_JWT' \
  -H 'content-type: application/json' \
  -d '{
  "gene": ""
}'

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