Forge Tools modomics_modifications

modomics_modifications read

scidex.forge.modomics_modifications

Search the MODOMICS database (genesilico.pl/modomics) for RNA modification records. MODOMICS is the reference catalog for chemical RNA modifications, covering >170 distinct modifications across all RNA classes. Each record includes the short symbol (m1A, m6A, psi), full name, molecular formula, modification type (methylation, pseudouridylation, acetylation, …), affected nucleotide base (A/C/G/U), KEGG/PubChem/ChEBI cross-references, and biosynthetic enzymes. Query by modification symbol (m6A), chemical class (methylation), or nucleotide class (A). An empty query returns all modifications up to the limit. REST API: https://genesilico.pl/modomics/api/modifications/ — free, no auth required.

HTTP: POST /api/scidex/forge/modomics_modifications

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.modomics_modifications``.",
  "properties": {
    "query": {
      "default": "",
      "description": "Search term for RNA modifications. Matched case-insensitively against short_name (e.g. 'm6A'), name, modification_type (e.g. 'methylation'), and moiety_class (e.g. 'A'). An empty string returns all entries up to limit.",
      "maxLength": 500,
      "title": "Query",
      "type": "string"
    },
    "limit": {
      "default": 20,
      "description": "Maximum number of modifications to return (default 20, max 100).",
      "maximum": 100,
      "minimum": 1,
      "title": "Limit",
      "type": "integer"
    }
  },
  "title": "ForgeModomicsModificationsIn",
  "type": "object"
}
Output schema 
{
  "$defs": {
    "ModomicsModification": {
      "description": "One MODOMICS RNA modification record.",
      "properties": {
        "short_name": {
          "description": "Abbreviated symbol for the modification (e.g. 'm1A', 'm6A', 'psi').",
          "title": "Short Name",
          "type": "string"
        },
        "name": {
          "default": "",
          "description": "Full common or IUPAC name of the modification.",
          "title": "Name",
          "type": "string"
        },
        "formula": {
          "default": "",
          "description": "Molecular formula (e.g. 'C10H13N5O4').",
          "title": "Formula",
          "type": "string"
        },
        "modification_type": {
          "default": "",
          "description": "Chemical modification class (e.g. 'methylation', 'pseudouridylation').",
          "title": "Modification Type",
          "type": "string"
        },
        "moiety_class": {
          "default": "",
          "description": "Affected nucleotide base class (e.g. 'A', 'C', 'G', 'U').",
          "title": "Moiety Class",
          "type": "string"
        },
        "kegg_id": {
          "default": "",
          "description": "KEGG compound identifier.",
          "title": "Kegg Id",
          "type": "string"
        },
        "pubchem_id": {
          "default": "",
          "description": "PubChem compound identifier.",
          "title": "Pubchem Id",
          "type": "string"
        },
        "chebi_id": {
          "default": "",
          "description": "ChEBI ontology identifier.",
          "title": "Chebi Id",
          "type": "string"
        },
        "nucleotide": {
          "default": "",
          "description": "Parent nucleotide being modified.",
          "title": "Nucleotide",
          "type": "string"
        },
        "enzymes": {
          "description": "Names of biosynthetic or pathway enzymes associated with this modification.",
          "items": {
            "type": "string"
          },
          "title": "Enzymes",
          "type": "array"
        }
      },
      "required": [
        "short_name"
      ],
      "title": "ModomicsModification",
      "type": "object"
    }
  },
  "description": "Response shape for ``scidex.forge.modomics_modifications``.",
  "properties": {
    "query": {
      "description": "The search query submitted.",
      "title": "Query",
      "type": "string"
    },
    "modifications": {
      "description": "RNA modification records from MODOMICS matching the query.",
      "items": {
        "$ref": "#/$defs/ModomicsModification"
      },
      "title": "Modifications",
      "type": "array"
    },
    "not_found": {
      "default": false,
      "description": "True if no modifications matched the query.",
      "title": "Not Found",
      "type": "boolean"
    },
    "source": {
      "default": "MODOMICS",
      "description": "Data source identifier.",
      "title": "Source",
      "type": "string"
    }
  },
  "required": [
    "query"
  ],
  "title": "ForgeModomicsModificationsOut",
  "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/modomics_modifications' \
  -H 'authorization: Bearer $SCIDEX_JWT' \
  -H 'content-type: application/json' \
  -d '{}'

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