Forge Tools hmdb_metabolites

hmdb_metabolites read

scidex.forge.hmdb_metabolites

Query the Human Metabolome Database (HMDB, 217,920 entries) by metabolite name or HMDB accession ID. Returns metabolite properties (formula, mass, IUPAC name, InChIKey, SMILES), biofluid and tissue locations, metabolic pathways, disease associations, protein interactions, and cross-references to PubChem, ChEBI, and KEGG. Complements forge_pubchem_compound (chemistry) and forge_chebi_compound (ontology) with metabolome-specific biology and disease context. REST API: https://hmdb.ca — free, no auth required.

HTTP: POST /api/scidex/forge/hmdb_metabolites

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.hmdb_metabolites``.",
  "properties": {
    "metabolite_name": {
      "default": "",
      "description": "Common or IUPAC metabolite name to search (e.g. ``glucose``, ``lactate``, ``creatine``). At least one of metabolite_name or hmdb_ids is required.",
      "maxLength": 300,
      "title": "Metabolite Name",
      "type": "string"
    },
    "hmdb_ids": {
      "description": "List of HMDB accession IDs for direct lookup (e.g. ``['HMDB0000122']``). At least one of metabolite_name or hmdb_ids is required.",
      "items": {
        "type": "string"
      },
      "maxItems": 50,
      "title": "Hmdb Ids",
      "type": "array"
    },
    "limit": {
      "default": 10,
      "description": "Maximum number of metabolites to return (default 10, max 50).",
      "maximum": 50,
      "minimum": 1,
      "title": "Limit",
      "type": "integer"
    }
  },
  "title": "ForgeHMDBIn",
  "type": "object"
}
Output schema 
{
  "$defs": {
    "HMDBMetabolite": {
      "description": "One HMDB metabolite record.",
      "properties": {
        "hmdb_id": {
          "description": "HMDB accession (e.g. HMDB0000122).",
          "title": "Hmdb Id",
          "type": "string"
        },
        "name": {
          "description": "Preferred HMDB name.",
          "title": "Name",
          "type": "string"
        },
        "synonyms": {
          "description": "Known synonyms.",
          "items": {
            "type": "string"
          },
          "title": "Synonyms",
          "type": "array"
        },
        "chemical_formula": {
          "default": "",
          "description": "Molecular formula (e.g. C6H12O6).",
          "title": "Chemical Formula",
          "type": "string"
        },
        "monoisotopic_mass": {
          "anyOf": [
            {
              "type": "number"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "Monoisotopic molecular weight in Da.",
          "title": "Monoisotopic Mass"
        },
        "average_mass": {
          "anyOf": [
            {
              "type": "number"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "Average molecular weight in Da.",
          "title": "Average Mass"
        },
        "iupac_name": {
          "default": "",
          "description": "IUPAC systematic name.",
          "title": "Iupac Name",
          "type": "string"
        },
        "inchi_key": {
          "default": "",
          "description": "InChIKey identifier.",
          "title": "Inchi Key",
          "type": "string"
        },
        "smiles": {
          "default": "",
          "description": "SMILES string.",
          "title": "Smiles",
          "type": "string"
        },
        "biofluid_locations": {
          "description": "Biofluids where this metabolite is detected (e.g. Blood, Urine, CSF).",
          "items": {
            "type": "string"
          },
          "title": "Biofluid Locations",
          "type": "array"
        },
        "tissue_locations": {
          "description": "Tissues where this metabolite is detected (e.g. Liver, Brain).",
          "items": {
            "type": "string"
          },
          "title": "Tissue Locations",
          "type": "array"
        },
        "pathways": {
          "description": "Metabolic pathway names this metabolite participates in.",
          "items": {
            "type": "string"
          },
          "title": "Pathways",
          "type": "array"
        },
        "disease_associations": {
          "description": "Disease names associated with abnormal levels of this metabolite.",
          "items": {
            "type": "string"
          },
          "title": "Disease Associations",
          "type": "array"
        },
        "protein_associations": {
          "description": "Gene/protein names associated with this metabolite (transporters, enzymes).",
          "items": {
            "type": "string"
          },
          "title": "Protein Associations",
          "type": "array"
        },
        "pubchem_cid": {
          "default": "",
          "description": "PubChem Compound ID.",
          "title": "Pubchem Cid",
          "type": "string"
        },
        "chebi_id": {
          "default": "",
          "description": "ChEBI accession (e.g. CHEBI:17234).",
          "title": "Chebi Id",
          "type": "string"
        },
        "kegg_id": {
          "default": "",
          "description": "KEGG Compound ID (e.g. C00031).",
          "title": "Kegg Id",
          "type": "string"
        }
      },
      "required": [
        "hmdb_id",
        "name"
      ],
      "title": "HMDBMetabolite",
      "type": "object"
    }
  },
  "description": "Response shape for ``scidex.forge.hmdb_metabolites``.",
  "properties": {
    "query": {
      "description": "The metabolite name queried, or '' for ID lookups.",
      "title": "Query",
      "type": "string"
    },
    "metabolites": {
      "description": "Matching HMDB metabolite records.",
      "items": {
        "$ref": "#/$defs/HMDBMetabolite"
      },
      "title": "Metabolites",
      "type": "array"
    },
    "total_found": {
      "default": 0,
      "description": "Total metabolites found before the limit was applied.",
      "title": "Total Found",
      "type": "integer"
    },
    "took_ms": {
      "description": "Wall-clock time for the upstream calls.",
      "title": "Took Ms",
      "type": "integer"
    }
  },
  "required": [
    "query",
    "took_ms"
  ],
  "title": "ForgeHMDBOut",
  "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/hmdb_metabolites' \
  -H 'authorization: Bearer $SCIDEX_JWT' \
  -H 'content-type: application/json' \
  -d '{}'

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