Forge Tools omnipath_interactions

omnipath_interactions read

scidex.forge.omnipath_interactions

Query OmniPath for curated signaling and regulatory interactions aggregated from 100+ source databases (SIGNOR, IntAct, BioGRID, KEGG, Reactome, NCI-PID, and 90+ others). Supports post-translational, transcriptional, and miRNA interaction types. Returns interactions with source/target gene, effect (activation/inhibition), mechanism, multi-database provenance, and PubMed references. No authentication required.

HTTP: POST /api/scidex/forge/omnipath_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.omnipath_interactions``.",
  "properties": {
    "genes": {
      "description": "Gene symbols to query (e.g. ``['TP53', 'EGFR']``). OmniPath returns interactions where the gene is source or target. 1–20 gene symbols per call.",
      "items": {
        "type": "string"
      },
      "maxItems": 20,
      "minItems": 1,
      "title": "Genes",
      "type": "array"
    },
    "interaction_type": {
      "default": "post_translational",
      "description": "Interaction type category: ``'post_translational'`` (kinase-substrate, PTM events), ``'transcriptional'`` (TF→target gene), ``'mirna'`` (miRNA post-transcriptional), ``'all'`` (all combined).",
      "enum": [
        "post_translational",
        "transcriptional",
        "mirna",
        "all"
      ],
      "title": "Interaction Type",
      "type": "string"
    },
    "directed_only": {
      "default": false,
      "description": "When True, return only directed interactions (is_directed=True).",
      "title": "Directed Only",
      "type": "boolean"
    },
    "signed_only": {
      "default": false,
      "description": "When True, return only interactions with a known stimulation or inhibition sign (excludes sign-unknown records).",
      "title": "Signed Only",
      "type": "boolean"
    },
    "min_sources": {
      "default": 1,
      "description": "Minimum number of distinct source databases required. Higher values yield higher-confidence interactions. Default 1.",
      "maximum": 100,
      "minimum": 1,
      "title": "Min Sources",
      "type": "integer"
    },
    "limit": {
      "default": 50,
      "description": "Maximum number of interaction records to return. Default 50.",
      "maximum": 500,
      "minimum": 1,
      "title": "Limit",
      "type": "integer"
    }
  },
  "required": [
    "genes"
  ],
  "title": "ForgeOmniPathIn",
  "type": "object"
}
Output schema 
{
  "$defs": {
    "OmniPathInteraction": {
      "description": "One OmniPath interaction record with multi-database provenance.",
      "properties": {
        "source_gene": {
          "description": "Gene symbol of the upstream / regulatory entity.",
          "title": "Source Gene",
          "type": "string"
        },
        "target_gene": {
          "description": "Gene symbol of the downstream / regulated entity.",
          "title": "Target Gene",
          "type": "string"
        },
        "effect": {
          "default": "",
          "description": "Causal effect of the interaction: 'activation', 'inhibition', 'unknown', or ''.",
          "title": "Effect",
          "type": "string"
        },
        "mechanism": {
          "default": "",
          "description": "Molecular mechanism (e.g. 'phosphorylation', 'ubiquitination', 'transcriptional regulation').  May be empty when not reported.",
          "title": "Mechanism",
          "type": "string"
        },
        "is_directed": {
          "default": false,
          "description": "True when the interaction has an annotated direction (source → target).",
          "title": "Is Directed",
          "type": "boolean"
        },
        "is_stimulation": {
          "default": false,
          "description": "True when the interaction is annotated as an activation/stimulation.",
          "title": "Is Stimulation",
          "type": "boolean"
        },
        "is_inhibition": {
          "default": false,
          "description": "True when the interaction is annotated as an inhibition.",
          "title": "Is Inhibition",
          "type": "boolean"
        },
        "databases": {
          "description": "Source databases that reported this interaction (e.g. ['SIGNOR', 'IntAct', 'BioGRID']).",
          "items": {
            "type": "string"
          },
          "title": "Databases",
          "type": "array"
        },
        "references": {
          "description": "PubMed IDs or other references supporting this interaction.",
          "items": {
            "type": "string"
          },
          "title": "References",
          "type": "array"
        },
        "n_sources": {
          "default": 0,
          "description": "Number of distinct source databases reporting this interaction.",
          "title": "N Sources",
          "type": "integer"
        }
      },
      "required": [
        "source_gene",
        "target_gene"
      ],
      "title": "OmniPathInteraction",
      "type": "object"
    }
  },
  "description": "Response shape for ``scidex.forge.omnipath_interactions``.",
  "properties": {
    "interactions": {
      "description": "Interaction records matching the query after all filters. Empty when the queried genes have no interactions in OmniPath.",
      "items": {
        "$ref": "#/$defs/OmniPathInteraction"
      },
      "title": "Interactions",
      "type": "array"
    },
    "total_found": {
      "description": "Total matching interactions before applying the ``limit`` (after directed/signed/min_sources filters).",
      "title": "Total Found",
      "type": "integer"
    },
    "not_found": {
      "default": false,
      "description": "True when none of the queried genes appear in OmniPath (upstream API returned an empty result set).",
      "title": "Not Found",
      "type": "boolean"
    }
  },
  "required": [
    "total_found"
  ],
  "title": "ForgeOmniPathOut",
  "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/omnipath_interactions' \
  -H 'authorization: Bearer $SCIDEX_JWT' \
  -H 'content-type: application/json' \
  -d '{
  "genes": []
}'

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