Forge Tools biogrid_interactions

biogrid_interactions read

scidex.forge.biogrid_interactions

Query BioGRID for manually curated protein-protein and genetic interactions. Returns experimentally validated edges with source publication (PubMed), experimental system, and throughput category. Complements high-throughput STRING PPI data with low-throughput curated evidence from 400K+ publications.

HTTP: POST /api/scidex/forge/biogrid_interactions

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.biogrid_interactions``.",
  "properties": {
    "gene_names": {
      "description": "Gene symbols to query (e.g. ``['BRCA1', 'TP53']``). BioGRID returns interactions where at least one interactor matches. 1–10 genes per call.",
      "items": {
        "type": "string"
      },
      "maxItems": 10,
      "minItems": 1,
      "title": "Gene Names",
      "type": "array"
    },
    "species_id": {
      "default": 9606,
      "description": "NCBI Taxonomy ID. Defaults to 9606 (Homo sapiens). Common alternates: 10090 (Mus musculus), 10116 (Rattus norvegicus), 7227 (Drosophila melanogaster), 6239 (C. elegans).",
      "maximum": 10000000,
      "minimum": 1,
      "title": "Species Id",
      "type": "integer"
    },
    "interaction_type": {
      "default": "physical",
      "description": "Interaction class to return: ``'physical'`` (protein-protein, co-immunoprecipitation, two-hybrid, …) or ``'genetic'`` (synthetic lethality, epistasis, …). Matched against the ``EXPERIMENTAL_SYSTEM_TYPE`` field in BioGRID records.",
      "title": "Interaction Type",
      "type": "string"
    },
    "experimental_system": {
      "anyOf": [
        {
          "maxLength": 100,
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "Optional server-side filter by exact experimental system name, e.g. ``'Two-hybrid'``, ``'Co-immunoprecipitation'``. When set, BioGRID restricts results to that system before returning them. Case-sensitive; use BioGRID canonical names.",
      "title": "Experimental System"
    },
    "limit": {
      "default": 50,
      "description": "Maximum number of interaction records to return. Default 50.",
      "maximum": 200,
      "minimum": 1,
      "title": "Limit",
      "type": "integer"
    }
  },
  "required": [
    "gene_names"
  ],
  "title": "ForgeBioGRIDIn",
  "type": "object"
}
Output schema 
{
  "$defs": {
    "BioGRIDEdge": {
      "description": "One BioGRID interaction edge in the response.",
      "properties": {
        "gene_a": {
          "description": "Official gene symbol for interactor A.",
          "title": "Gene A",
          "type": "string"
        },
        "gene_b": {
          "description": "Official gene symbol for interactor B.",
          "title": "Gene B",
          "type": "string"
        },
        "experimental_system": {
          "default": "",
          "description": "Experimental system (e.g. 'Co-immunoprecipitation', 'Two-hybrid').",
          "title": "Experimental System",
          "type": "string"
        },
        "throughput": {
          "default": "",
          "description": "'Low Throughput', 'High Throughput', or 'Any Throughput'.",
          "title": "Throughput",
          "type": "string"
        },
        "pubmed_id": {
          "default": "",
          "description": "PubMed ID of the source publication.",
          "title": "Pubmed Id",
          "type": "string"
        },
        "score": {
          "default": "-",
          "description": "Interaction score (BioGRID reports '-' when not applicable).",
          "title": "Score",
          "type": "string"
        }
      },
      "required": [
        "gene_a",
        "gene_b"
      ],
      "title": "BioGRIDEdge",
      "type": "object"
    }
  },
  "description": "Response shape for ``scidex.forge.biogrid_interactions``.",
  "properties": {
    "interactions": {
      "description": "Curated interaction records matching the query.",
      "items": {
        "$ref": "#/$defs/BioGRIDEdge"
      },
      "title": "Interactions",
      "type": "array"
    },
    "total_count": {
      "description": "Total interactions found after filtering but before limit.",
      "title": "Total Count",
      "type": "integer"
    }
  },
  "required": [
    "total_count"
  ],
  "title": "ForgeBioGRIDOut",
  "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/biogrid_interactions' \
  -H 'authorization: Bearer $SCIDEX_JWT' \
  -H 'content-type: application/json' \
  -d '{
  "gene_names": []
}'

Discussion

Posting anonymously. Sign in for attribution.

No comments yet — be the first.