# `pubchem__pubchem_get_compound_xrefs`
**Get Compound Cross-References**
Get external database cross-references for a compound: PubMed citations, patent IDs, gene/protein associations, registry numbers, and taxonomy IDs. Results are paged per type — capped at maxPerType with the total count reported; reach the IDs past a page with offset.
- Server: [PubChem](https://gateway.mcpharbor.dev/docs/servers/pubchem) (`dev.mcpharbor.gateway/pubchem`)
- Price per call: $0.0001 (100 micro-USD); only tools/call is charged
- Endpoint: `https://gateway.mcpharbor.dev/mcp` or `https://gateway.mcpharbor.dev/mcp/pubchem`
- Upstream tool: exposed by the provider; called through this gateway as `pubchem__pubchem_get_compound_xrefs`
- Provider terms: (verified 2026-09-19)
- Upstream API documentation:
- Rate limit: 350 requests per minute
- Attribution required: Attribution to source recommended, not mandatory
## Parameters
- `cid` (integer, required): PubChem Compound ID. Resolve from name/SMILES with pubchem_search_compounds.
- `maxPerType` (integer, optional): Max IDs to return per xref type per page (1-500). A compound may have thousands of PubMed references; use offset to reach the ones past this page. Total count always reported. Default: 50. Default: `50`.
- `offset` (integer, optional): Zero-based index of the first ID to return within each xref type. The same offset is applied to every requested type. Pass the nextOffset from a previous call to read the following page. Default: 0. Default: `0`.
- `xrefTypes` (array, required): 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), T...
## Example call
Request headers and body:
```http
POST /mcp HTTP/1.1
Host: gateway.mcpharbor.dev
Authorization: Bearer
Content-Type: application/json
Accept: application/json, text/event-stream
MCP-Protocol-Version: 2026-07-28
Mcp-Method: tools/call
Mcp-Name: pubchem__pubchem_get_compound_xrefs
```
```json
{
"id": 1,
"jsonrpc": "2.0",
"method": "tools/call",
"params": {
"_meta": {
"io.modelcontextprotocol/clientCapabilities": {},
"io.modelcontextprotocol/clientInfo": {
"name": "example-agent",
"version": "1.0.0"
},
"io.modelcontextprotocol/protocolVersion": "2026-07-28"
},
"arguments": {
"cid": 1,
"xrefTypes": []
},
"name": "pubchem__pubchem_get_compound_xrefs"
}
}
```
A successful response:
```json
{
"id": 1,
"jsonrpc": "2.0",
"result": {
"_meta": {
"dev.mcpharbor.gateway/call": {
"chargedMicroUsd": 100,
"id": ""
}
},
"content": [
{
"text": "",
"type": "text"
}
],
"resultType": "complete"
}
}
```
This call costs $0.0001 (100 micro-USD). Reading this page and listing the tool cost nothing.
The `dev.mcpharbor.gateway/call` record in the result is the receipt for that charge. Each
POST is metered separately, so sending the same call again buys another one: see
[agent.txt](https://gateway.mcpharbor.dev/agent.txt), section 7, before retrying.
## Attribution
This provider requires the attribution below wherever you use results from its tools.
Reproduce it verbatim:
> Attribution to source recommended, not mandatory
## Tool definition
Exactly as `tools/list` returns it (free):
```json
{
"_meta": {
"dev.mcpharbor.gateway/pricing": {
"currency": "USD",
"pricePerCallMicroUsd": 100
}
},
"annotations": {
"idempotentHint": true,
"openWorldHint": true,
"readOnlyHint": true
},
"description": "Get external database cross-references for a compound: PubMed citations, patent IDs, gene/protein associations, registry numbers, and taxonomy IDs. Results are paged per type — capped at maxPerType with the total count reported; reach the IDs past a page with offset.",
"inputSchema": {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"additionalProperties": false,
"properties": {
"cid": {
"description": "PubChem Compound ID. Resolve from name/SMILES with pubchem_search_compounds.",
"exclusiveMinimum": 0,
"maximum": 9007199254740991,
"type": "integer"
},
"maxPerType": {
"default": 50,
"description": "Max IDs to return per xref type per page (1-500). A compound may have thousands of PubMed references; use offset to reach the ones past this page. Total count always reported. Default: 50.",
"maximum": 500,
"minimum": 1,
"type": "integer"
},
"offset": {
"default": 0,
"description": "Zero-based index of the first ID to return within each xref type. The same offset is applied to every requested type. Pass the nextOffset from a previous call to read the following page. Default: 0.",
"maximum": 9007199254740991,
"minimum": 0,
"type": "integer"
},
"xrefTypes": {
"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.",
"items": {
"enum": [
"RegistryID",
"RN",
"PubMedID",
"PatentID",
"GeneID",
"ProteinGI",
"TaxonomyID"
],
"type": "string"
},
"minItems": 1,
"type": "array"
}
},
"required": [
"cid",
"xrefTypes"
],
"type": "object"
},
"name": "pubchem__pubchem_get_compound_xrefs",
"outputSchema": {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"additionalProperties": false,
"anyOf": [
{
"not": {
"required": [
"error"
]
},
"required": [
"cid",
"xrefs",
"offset",
"truncated"
]
},
{
"required": [
"error"
]
}
],
"properties": {
"cid": {
"description": "PubChem Compound ID.",
"type": "number"
},
"error": {
"additionalProperties": {},
"description": "Present when the call failed. Absent on success.",
"properties": {
"code": {
"description": "JSON-RPC error code for this failure.",
"maximum": 9007199254740991,
"minimum": -9007199254740991,
"type": "integer"
},
"data": {
"additionalProperties": {},
"properties": {
"reason": {
"description": "Machine-readable failure mode.",
"type": "string"
},
"recovery": {
"additionalProperties": {},
"description": "Actionable next step for the caller.",
"properties": {
"hint": {
"type": "string"
}
},
"required": [
"hint"
],
"type": "object"
},
"retryable": {
"description": "Whether retrying may succeed.",
"type": "boolean"
}
},
"type": "object"
},
"message": {
"description": "Human-readable description of what went wrong.",
"type": "string"
}
},
"required": [
"code",
"message"
],
"type": "object"
},
"nextOffset": {
"description": "Offset to pass on the next call to continue past this page. Omitted when no requested type has further IDs.",
"type": "number"
},
"notice": {
"description": "Recovery guidance when every requested xref type returned zero IDs, when the offset runs past every type, or when further pages remain. Absent when this page is complete and non-empty.",
"type": "string"
},
"offset": {
"description": "Zero-based index of the first ID returned within each type.",
"type": "number"
},
"truncated": {
"description": "True when at least one requested type has IDs remaining past this page. Which types, and how many IDs each holds in total, is in xrefs[].truncated / xrefs[].totalAvailable.",
"type": "boolean"
},
"xrefs": {
"description": "Cross-references grouped by type.",
"items": {
"additionalProperties": false,
"description": "Cross-reference group for one type.",
"properties": {
"ids": {
"description": "Cross-reference IDs on this page (window of offset + maxPerType).",
"items": {
"anyOf": [
{
"description": "String-form cross-reference ID (e.g. CAS number, patent).",
"type": "string"
},
{
"description": "Numeric cross-reference ID (e.g. PubMed ID, Gene ID).",
"type": "number"
}
],
"description": "Cross-reference identifier — string or number depending on type."
},
"type": "array"
},
"totalAvailable": {
"description": "Total IDs available for this type, across all pages.",
"type": "number"
},
"truncated": {
"description": "True when IDs for this type remain past the current page.",
"type": "boolean"
},
"type": {
"description": "Cross-reference type: RegistryID, RN, PubMedID, PatentID, GeneID, ProteinGI, or TaxonomyID.",
"type": "string"
}
},
"required": [
"type",
"ids",
"totalAvailable",
"truncated"
],
"type": "object"
},
"type": "array"
}
},
"type": "object"
},
"title": "Get Compound Cross-References"
}
```