Skip to main content
Glama

Get Compound Cross-References

pubchem_get_compound_xrefs
Read-onlyIdempotent

Retrieve external cross-references for PubChem compounds. Access PubMed citations, patent IDs, gene/protein associations, and registry numbers with configurable limits and total counts.

Instructions

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.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
cidYesPubChem Compound ID.
xrefTypesYesCross-reference types to retrieve. Options: RegistryID, RN (CAS numbers), PubMedID, PatentID, GeneID, ProteinGI, TaxonomyID.
maxPerTypeNoMax IDs to return per xref type (1-500). A compound may have thousands of PubMed references — this cap prevents bloat. Total count always reported. Default: 50.

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
cidYesPubChem Compound ID.
xrefsYesCross-references grouped by type.
Behavior4/5

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

While annotations declare read-only and idempotent characteristics, the description adds crucial behavioral context: 'Results are capped per type with total counts reported.' This explains the limiting behavior and response structure beyond what annotations provide, though it omits rate limits or error conditions.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness5/5

Is the description appropriately sized, front-loaded, and free of redundancy?

Two sentences total with zero waste. The first front-loads the core purpose and data types; the second provides essential behavioral constraints. Every word earns its place.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness4/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

Given the presence of an output schema and comprehensive input schema, the description appropriately focuses on purpose and behavioral quirks (capping) rather than return values. It adequately covers the tool's scope for a read-only lookup operation, though it could mention external service dependencies implied by openWorldHint.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters3/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

With 100% schema description coverage, the schema fully documents all parameters including the rationale for maxPerType ('prevents bloat'). The description lists the xref types but does not add semantic meaning beyond what the schema already provides, warranting the baseline score for high-coverage schemas.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose5/5

Does the description clearly state what the tool does and how it differs from similar tools?

The description states a specific verb ('Get') and resource ('external database cross-references') and enumerates the exact xref types retrieved (PubMed, patents, genes, etc.). This clearly distinguishes it from siblings like get_compound_details (general metadata) or get_compound_image (visual data).

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines3/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

The description implies usage through the list of xref types (use when you need PubMed citations, patents, etc.), but provides no explicit when-to-use guidance, when-not-to-use warnings, or named alternatives among the sibling tools.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.

Install Server

Other Tools

Latest Blog Posts

MCP directory API

We provide all the information about MCP servers via our MCP API.

curl -X GET 'https://glama.ai/api/mcp/v1/servers/cyanheads/pubchem-mcp-server'

If you have feedback or need assistance with the MCP directory API, please join our Discord server