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pubchem-mcp-server

by io.github.cyanheads

Get Compound Cross-References

pubchem_get_compound_xrefs
Read-onlyIdempotent

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.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
cidYesPubChem Compound ID. Resolve from name/SMILES with pubchem_search_compounds.
offsetNoZero-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.
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 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.

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
cidNoPubChem Compound ID.
errorNoPresent when the call failed. Absent on success.
xrefsNoCross-references grouped by type.
noticeNoRecovery 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.
offsetNoZero-based index of the first ID returned within each type.
truncatedNoTrue 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.
nextOffsetNoOffset to pass on the next call to continue past this page. Omitted when no requested type has further IDs.

TDQS

A4.5/5.0
Behavior4/5

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

Annotations already declare readOnlyHint and idempotentHint, so the safety profile is covered. The description adds the paging behavior (capped at maxPerType, total count reported, offset to read further) which the agent needs to know to correctly iterate results. It doesn't contradict any annotation. Doesn't describe return format, but output schema covers that. A 4 is fair because the description adds meaningful behavioral context beyond the 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?

Two sentences, front-loaded with the primary purpose, then a compact explanation of paging. No filler, every word earns its place.

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?

With a 100% parameter schema coverage and a returned output schema, the description covers purpose, scope, and paging behavior. Nothing an agent needs in order to call it correctly is missing.

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

Parameters4/5

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

Schema coverage is 100% with detailed per-parameter descriptions, including the semantics of xrefTypes enumerations Continued. The description adds the cross-type paging model ('Results are paged per type') which clarifies how maxPerType and offset interact across multiple requested types. This goes beyond the schema property descriptions. A 4 reflects that added meaning.

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 external database cross-references'), names the resource ('a compound'), and enumerates the specific cross-reference types (PubMed citations, patent IDs, gene/protein associations, registry numbers, taxonomy IDs). This is unambiguous and distinguishes the tool from siblings like pubchem_get_compound_properties without needing to inspect the schema.

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

Usage Guidelines4/5

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

The description clearly scopes when to use this tool ('external database cross-references') and notes the paging behavior for large result sets. It doesn't explicitly name alternative tools for non-xref data like 3D structures or synonyms, but the tool name and the clear focus imply the boundary. No explicit exclusion of alternatives, so a 4 rather than 5.

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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TDQS

A4.3/5.0
Disambiguation4/5

Tools cleanly separate into search (compounds, assays) and retrieval (details, structure, image, safety, xrefs, bioactivity, interactions, summary). The only mild overlap is bioactivity versus interactions, but their descriptions clarify that one focuses on assay outcomes and the other on drug-drug/food/chemical-target records.

Naming Consistency5/5

All tools follow a consistent pubchem_<verb>_<object> pattern, with get_ for retrieval and search_ for discovery. Minor variations like pubchem_get_summary still fit the same convention clearly.

Tool Count5/5

Ten tools is well-scoped for a PubChem client: search entry points, compound detail retrieval, structural representations, safety data, interaction data, and cross-reference lookups. Each tool earns its place without redundancy.

Completeness5/5

The surface covers the core PubChem workflows: finding compounds and assays, retrieving compound properties and structures, and exploring bioactivity, safety, interactions, and cross-references. Search results feed directly into retrieval tools, and paging is provided where needed, leaving no obvious dead ends.

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