Forge Tools monarch_initiative

monarch_initiative read

scidex.forge.monarch_initiative

Query the Monarch Initiative knowledge graph for disease-gene-phenotype associations. Accepts a gene symbol (HGNC), disease ID (OMIM/Orphanet), or HPO phenotype term (HP:). Returns subject-predicate-object associations with frequency qualifiers, onset qualifiers, and provenance sources from 33+ integrated databases (OMIM, HPOA, MGI, ZFIN, Orphanet). Complements disgenet (human-only) and hpo_phenotype (ontology-only) with cross-species multi-source phenotype-gene associations. API: api.monarchinitiative.org — public, no auth.

HTTP: POST /api/scidex/forge/monarch_initiative

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.monarch_initiative``.",
  "properties": {
    "query": {
      "description": "Entity to query. For ``query_type='gene'``: HGNC gene symbol (e.g. ``'BRCA2'``). For ``query_type='disease'``: OMIM or Orphanet ID (e.g. ``'OMIM:154700'``). For ``query_type='phenotype'``: HP: term ID (e.g. ``'HP:0001250'``).",
      "maxLength": 200,
      "title": "Query",
      "type": "string"
    },
    "query_type": {
      "default": "gene",
      "description": "Type of the query entity. One of ``'gene'`` (HGNC symbol), ``'disease'`` (OMIM/Orphanet ID), or ``'phenotype'`` (HP: term).",
      "title": "Query Type",
      "type": "string"
    },
    "association_types": {
      "description": "Optional Biolink category filter for association types (e.g. ``['biolink:GeneToDiseaseAssociation']``). Empty list returns all association types.",
      "items": {
        "type": "string"
      },
      "maxItems": 5,
      "title": "Association Types",
      "type": "array"
    },
    "limit": {
      "default": 20,
      "description": "Maximum number of associations to return. Default 20.",
      "maximum": 100,
      "minimum": 1,
      "title": "Limit",
      "type": "integer"
    },
    "include_phenotypes": {
      "default": true,
      "description": "When True (default), include phenotype-related associations alongside disease associations.",
      "title": "Include Phenotypes",
      "type": "boolean"
    }
  },
  "required": [
    "query"
  ],
  "title": "ForgeMonarchIn",
  "type": "object"
}
Output schema 
{
  "$defs": {
    "MonarchAssociation": {
      "description": "One association record from the Monarch Initiative.",
      "properties": {
        "subject_id": {
          "description": "Subject entity ID (e.g. ``'HGNC:1100'``).",
          "title": "Subject Id",
          "type": "string"
        },
        "subject_label": {
          "default": "",
          "description": "Subject entity label.",
          "title": "Subject Label",
          "type": "string"
        },
        "subject_category": {
          "default": "",
          "description": "Biolink category of subject.",
          "title": "Subject Category",
          "type": "string"
        },
        "object_id": {
          "description": "Object entity ID (e.g. ``'MONDO:0007254'``).",
          "title": "Object Id",
          "type": "string"
        },
        "object_label": {
          "default": "",
          "description": "Object entity label.",
          "title": "Object Label",
          "type": "string"
        },
        "object_category": {
          "default": "",
          "description": "Biolink category of object.",
          "title": "Object Category",
          "type": "string"
        },
        "predicate": {
          "default": "",
          "description": "Biolink predicate (e.g. ``'biolink:gene_associated_with_condition'``).",
          "title": "Predicate",
          "type": "string"
        },
        "frequency": {
          "anyOf": [
            {
              "type": "string"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "Frequency qualifier (HP: term or label), if recorded.",
          "title": "Frequency"
        },
        "onset": {
          "anyOf": [
            {
              "type": "string"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "Onset qualifier (HP: term or label), if recorded.",
          "title": "Onset"
        },
        "sources": {
          "description": "Provenance knowledge sources (e.g. ``['infores:omim']``).",
          "items": {
            "type": "string"
          },
          "title": "Sources",
          "type": "array"
        }
      },
      "required": [
        "subject_id",
        "object_id"
      ],
      "title": "MonarchAssociation",
      "type": "object"
    }
  },
  "description": "Response shape for ``scidex.forge.monarch_initiative``.",
  "properties": {
    "associations": {
      "description": "Disease-gene-phenotype associations from Monarch Initiative.",
      "items": {
        "$ref": "#/$defs/MonarchAssociation"
      },
      "title": "Associations",
      "type": "array"
    },
    "took_ms": {
      "description": "Wall-clock time for all upstream API calls.",
      "title": "Took Ms",
      "type": "integer"
    }
  },
  "required": [
    "took_ms"
  ],
  "title": "ForgeMonarchOut",
  "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/monarch_initiative' \
  -H 'authorization: Bearer $SCIDEX_JWT' \
  -H 'content-type: application/json' \
  -d '{
  "query": ""
}'

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