Forge Tools genemania

genemania read

scidex.forge.genemania

Query the GeneMANIA gene functional association network for predicted functional partners of a set of query genes. Returns associated genes ranked by Bayesian coupling score across co-expression, genetic interaction, pathway co-membership, protein domain similarity, and physical interaction evidence channels. Complements STRING PPI (edge-centric) by adding co-expression and pathway context via Bayesian network integration. Input: gene_symbols (HGNC, 1–20 genes), organism (default 'Homo sapiens'), max_results (default 20). API: POST https://genemania.org/api/search/ (free, no auth).

HTTP: POST /api/scidex/forge/genemania

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.genemania``.",
  "properties": {
    "gene_symbols": {
      "description": "HGNC gene symbols to query (e.g. ``['TP53', 'BRCA1']``). Accepts 1–20 genes. GeneMANIA will predict functional partners for the entire set jointly, not per-gene.",
      "items": {
        "type": "string"
      },
      "maxItems": 20,
      "minItems": 1,
      "title": "Gene Symbols",
      "type": "array"
    },
    "organism": {
      "default": "Homo sapiens",
      "description": "Organism for the query. GeneMANIA supports: 'Homo sapiens' (default), 'Mus musculus', 'Rattus norvegicus', 'Saccharomyces cerevisiae', 'Drosophila melanogaster', 'Caenorhabditis elegans', 'Danio rerio', 'Arabidopsis thaliana'.",
      "maxLength": 100,
      "title": "Organism",
      "type": "string"
    },
    "max_results": {
      "default": 20,
      "description": "Maximum number of associated genes to return. GeneMANIA ranks results by Bayesian association score descending. Default 20.",
      "maximum": 100,
      "minimum": 1,
      "title": "Max Results",
      "type": "integer"
    }
  },
  "required": [
    "gene_symbols"
  ],
  "title": "ForgeGeneManiaIn",
  "type": "object"
}
Output schema 
{
  "$defs": {
    "GeneManiaPrediction": {
      "description": "One GeneMANIA functional association prediction.",
      "properties": {
        "gene_symbol": {
          "description": "HGNC gene symbol for the predicted functional partner.",
          "title": "Gene Symbol",
          "type": "string"
        },
        "score": {
          "description": "Bayesian association score in [0, 1]. Higher values indicate stronger predicted functional coupling to the query gene set.",
          "maximum": 1,
          "minimum": 0,
          "title": "Score",
          "type": "number"
        },
        "networks": {
          "description": "Names of the evidence networks that contributed to this prediction (e.g. 'Co-expression', 'Physical Interactions', 'Pathway'). Non-empty for all scored predictions.",
          "items": {
            "type": "string"
          },
          "title": "Networks",
          "type": "array"
        }
      },
      "required": [
        "gene_symbol",
        "score"
      ],
      "title": "GeneManiaPrediction",
      "type": "object"
    }
  },
  "description": "Response shape for ``scidex.forge.genemania``.",
  "properties": {
    "associated_genes": {
      "description": "Predicted functional partners ranked by descending Bayesian association score. Empty when GeneMANIA finds no partners for the query gene set.",
      "items": {
        "$ref": "#/$defs/GeneManiaPrediction"
      },
      "title": "Associated Genes",
      "type": "array"
    },
    "not_found": {
      "description": "Query gene symbols not recognised by GeneMANIA for the specified organism. Partially-recognised queries still return results based on the genes that were found.",
      "items": {
        "type": "string"
      },
      "title": "Not Found",
      "type": "array"
    },
    "took_ms": {
      "default": 0,
      "description": "Wall-clock time for the upstream GeneMANIA API call.",
      "title": "Took Ms",
      "type": "integer"
    }
  },
  "title": "ForgeGeneManiaOut",
  "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/genemania' \
  -H 'authorization: Bearer $SCIDEX_JWT' \
  -H 'content-type: application/json' \
  -d '{
  "gene_symbols": []
}'

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