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pubchem_get_compound_xrefs

Active

Tool of pubchem-mcp-server

declared in 0.4.1

Get external database cross-references for a compound: PubMed citations, patent IDs, gene/protein associations, registry numbers, and taxonomy IDs. Results are capped per type with total counts reported.

Parameters schema

{
  "type": "object",
  "$schema": "http://json-schema.org/draft-07/schema#",
  "required": [
    "cid",
    "xrefTypes"
  ],
  "properties": {
    "cid": {
      "type": "integer",
      "maximum": 9007199254740991,
      "description": "PubChem Compound ID. Resolve from name/SMILES with pubchem_search_compounds.",
      "exclusiveMinimum": 0
    },
    "xrefTypes": {
      "type": "array",
      "items": {
        "enum": [
          "RegistryID",
          "RN",
          "PubMedID",
          "PatentID",
          "GeneID",
          "ProteinGI",
          "TaxonomyID"
        ],
        "type": "string"
      },
      "minItems": 1,
      "description": "Cross-reference types to retrieve. String IDs: RegistryID (DSSTox/EPA registry numbers), RN (CAS numbers), PatentID. Numeric IDs: PubMedID, GeneID (NCBI Gene), ProteinGI (legacy NCBI Protein GI), TaxonomyID."
    },
    "maxPerType": {
      "type": "number",
      "default": 50,
      "maximum": 500,
      "minimum": 1,
      "description": "Max IDs to return per xref type (1-500). A compound may have thousands of PubMed references. Total count always reported. Default: 50."
    }
  }
}

What this tool wraps· 1 endpoint

min confidence0.700.50

Parent server

pubchem-mcp-server

https://github.com/cyanheads/pubchem-mcp-server

3/7 registries
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pubchem_get_compound_xrefs — pubchem-mcp-server — PRSM MCP