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pubchem-mcp-server

by io.github.cyanheads

Get Bioactivity

pubchem_get_bioactivity
Read-onlyIdempotent

Get a compound's bioactivity profile: which assays tested it, activity outcomes (Active/Inactive/Inconclusive), target identifiers (NCBI Gene ID, UniProt/GenBank accession), and quantitative values (IC50, EC50, Ki, etc.). Filter by outcome and/or a specific molecular target (NCBI Gene ID or protein accession) to focus the profile — e.g. "is this compound active against target T?".

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
cidYesPubChem Compound ID. Resolve from name/SMILES with pubchem_search_compounds.
offsetNoZero-based index of the first assay to return, applied after the outcome and target filters. Pass the nextOffset from a previous call to read the following page. Default: 0.
maxResultsNoMax assay results to return per page (1-100). Well-studied compounds have thousands of records; use offset to reach the ones past this page. Default: 20.
targetGeneIdNoFilter to assays against this NCBI Gene ID. Obtain Gene IDs from pubchem_search_assays or the targetGeneId field of an unfiltered result here. Combine with outcomeFilter="active" to answer "is this compound active against target T?".
outcomeFilterNoFilter by activity outcome. "active" shows only assays where the compound showed activity — most useful for understanding biological profile. Default: "all".all
targetAccessionNoFilter to assays against this target protein accession (UniProt/GenBank), e.g. "P35354". Obtain accessions from pubchem_search_assays or the targetAccession field of an unfiltered result here.

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
capNoThe maxResults cap that was applied.
cidNoPubChem Compound ID.
errorNoPresent when the call failed. Absent on success.
shownNoAssays returned on this page.
noticeNoRecovery guidance when the filter yields no results or the compound has no bioactivity data.
offsetNoZero-based index of the first assay returned.
resultsNoAssay results matching the filter.
truncatedNoTrue when matching assays remain past this page.
nextOffsetNoOffset to pass on the next call to continue past this page. Omitted when no further assays match.
activeCountNoAssays with "Active" outcome.
totalAssaysNoTotal unique assays for this compound.
targetFilterNoTarget filter applied (gene ID and/or protein accession), when set.
filteredCountNoExact number of assays matching the outcome and target filters, across all pages.
inactiveCountNoAssays with "Inactive" outcome.
outcomeFilterNoOutcome filter applied: active, inactive, or all.
returnedCountNoAssays returned on this page.

TDQS

A4.3/5.0
Behavior3/5

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

The description mentions it returns quantitative values and identifiers, but doesn't specify the exact response format (e.g., whether it returns a list of assays with nested target info) or pagination behavior beyond mentioning offset. The readOnlyHint and idempotentHint are consistent with the read-only nature of the tool, but the description doesn't elaborate on potential response size or data structure.

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

Conciseness4/5

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

The description is concise and well-structured, with the core purpose stated first, then behavior details It avoids unnecessary verbosity while covering key aspects. The example question is helpful but could be seen as slightly redundant given the parameter descriptions, but it doesn't hurt.

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?

The description fully covers what the tool does and how to use it, including filtering and pagination. It doesn't mention potential edge cases (e.g., compound with no assays) or response schema details, but the schema is provided separatelyholistically. The tool is from a set (search compounds etc.), and the description references them appropriately.

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?

All parameters are described with types, defaults, and constraints in the schema apparent in the prompt. The description adds semantic guidance for offset (zero-based, after filters), maxResults (paginate for more), and targetGeneId (how to obtain it). Some fields like targetAccession are described but could use more detail on format, but overall strong.

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 clearly states what the tool does: retrieves a compound's bioactivity profile including assays, outcomes, targets, and quantitative values. It gives concrete examples (NCBI Gene ID, UniProt accession, IC50/EC50/Ki) and a use-case question, making the purpose immediately understandable.

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

Usage Guidelines5/5

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

The description explains how to filter by outcome and target, and gives a specific query example ('is this compound active against target T?'). The schema further clarifies pagination (offset, maxResults) and how to resolve Gene IDs using related tools, providing complete usage guidance.

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.

Resources