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Get Compound Cross-References

pubchem_get_compound_xrefs
Read-onlyIdempotent

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

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. Resolve from name/SMILES with pubchem_search_compounds.
xrefTypesYesCross-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.
maxPerTypeNoMax IDs to return per xref type (1-500). A compound may have thousands of PubMed references. 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?

Annotations already indicate readOnlyHint, idempotentHint, openWorldHint. The description adds useful behavioral context: results are capped per type and total counts are reported. No contradiction with annotations.

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?

Single sentence that front-loads purpose, lists types, and mentions capping. Every part is informative; no wasted words.

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

Completeness5/5

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

Given the complexity of multiple xref types and capping, the description covers essential behavior. Output schema handles return structure. The description is complete for a tool with rich schema and annotations.

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

Parameters5/5

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

Schema description coverage is 100%. Description adds meaning by explaining that cid can be resolved from name/SMILES using another tool, categorizing xrefTypes into string vs numeric IDs, and providing defaults and range for maxPerType. This goes beyond schema.

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?

Description uses specific verb 'Get' and identifies the resource as 'external database cross-references for a compound'. It lists specific types (PubMed citations, patent IDs, etc.) and mentions capping per type, clearly distinguishing it from sibling tools like pubchem_get_compound_details or pubchem_get_compound_safety.

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 when cross-references are needed but does not explicitly state when to use this tool versus alternatives. No mention of conditions for use or exclusions.

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

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