Forge Tools intact_interactions

intact_interactions read

scidex.forge.intact_interactions

Query IntAct (EMBL-EBI) for experimentally determined molecular interactions. Returns binary protein-protein, protein-RNA, and protein-small-molecule interactions with structured evidence: interaction type (PSI-MI), detection method, PubMed provenance, and MI-score confidence (0–1). Complements STRING (functional associations) and BioGRID (genetic interactions) with 1.4M curated interactions across all species.

HTTP: POST /api/scidex/forge/intact_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.intact_interactions``.",
  "properties": {
    "gene_symbols": {
      "description": "Gene symbols to query (e.g. ``['TP53', 'MDM2']``). IntAct returns interactions where at least one interactor matches. 1–10 gene symbols per call.",
      "items": {
        "type": "string"
      },
      "maxItems": 10,
      "minItems": 1,
      "title": "Gene Symbols",
      "type": "array"
    },
    "species": {
      "default": "Homo sapiens",
      "description": "Species name to filter interactions. Defaults to 'Homo sapiens'. Common alternates: 'Mus musculus', 'Drosophila melanogaster', 'Saccharomyces cerevisiae'.",
      "maxLength": 100,
      "title": "Species",
      "type": "string"
    },
    "interaction_type": {
      "default": "",
      "description": "Optional filter for PSI-MI interaction type short name (e.g. 'physical association', 'direct interaction'). Empty string returns all interaction types.",
      "maxLength": 100,
      "title": "Interaction Type",
      "type": "string"
    },
    "detection_method": {
      "default": "",
      "description": "Optional filter for PSI-MI detection method short name (e.g. 'two hybrid', 'anti bait coimmunoprecipitation'). Empty string returns all detection methods.",
      "maxLength": 100,
      "title": "Detection Method",
      "type": "string"
    },
    "limit": {
      "default": 20,
      "description": "Maximum number of interaction records to return. Default 20.",
      "maximum": 200,
      "minimum": 1,
      "title": "Limit",
      "type": "integer"
    }
  },
  "required": [
    "gene_symbols"
  ],
  "title": "ForgeIntActIn",
  "type": "object"
}
Output schema 
{
  "$defs": {
    "IntActInteraction": {
      "description": "One IntAct binary interaction record.",
      "properties": {
        "interaction_ac": {
          "default": "",
          "description": "IntAct accession for the interaction (e.g. 'EBI-1234567').",
          "title": "Interaction Ac",
          "type": "string"
        },
        "interactor_a": {
          "description": "Gene name or identifier for interactor A.",
          "title": "Interactor A",
          "type": "string"
        },
        "interactor_b": {
          "description": "Gene name or identifier for interactor B.",
          "title": "Interactor B",
          "type": "string"
        },
        "interaction_type": {
          "default": "",
          "description": "Interaction type short name (e.g. 'physical association', 'direct interaction').",
          "title": "Interaction Type",
          "type": "string"
        },
        "detection_method": {
          "default": "",
          "description": "Experimental detection method short name (e.g. 'two hybrid', 'coimmunoprecipitation').",
          "title": "Detection Method",
          "type": "string"
        },
        "pubmed_id": {
          "default": "",
          "description": "PubMed ID of the source publication.",
          "title": "Pubmed Id",
          "type": "string"
        },
        "confidence_score": {
          "anyOf": [
            {
              "type": "number"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "MI-score confidence (0.0–1.0). None when not reported by IntAct.",
          "title": "Confidence Score"
        },
        "experimental_roles": {
          "description": "Experimental roles assigned to interactors (e.g. ['bait', 'prey']).",
          "items": {
            "type": "string"
          },
          "title": "Experimental Roles",
          "type": "array"
        }
      },
      "required": [
        "interactor_a",
        "interactor_b"
      ],
      "title": "IntActInteraction",
      "type": "object"
    }
  },
  "description": "Response shape for ``scidex.forge.intact_interactions``.",
  "properties": {
    "interactions": {
      "description": "Interaction records from IntAct. Empty when no interactions are found for the given gene symbols at the requested filters.",
      "items": {
        "$ref": "#/$defs/IntActInteraction"
      },
      "title": "Interactions",
      "type": "array"
    },
    "total_found": {
      "description": "Total interactions reported by IntAct for this query (may exceed the number returned when limit < total).",
      "title": "Total Found",
      "type": "integer"
    }
  },
  "required": [
    "total_found"
  ],
  "title": "ForgeIntActOut",
  "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/intact_interactions' \
  -H 'authorization: Bearer $SCIDEX_JWT' \
  -H 'content-type: application/json' \
  -d '{
  "gene_symbols": []
}'

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