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Search Assays

pubchem_search_assays
Read-onlyIdempotent

Search PubChem bioassays by biological target. Enter a gene symbol, protein name, NCBI Gene ID, or UniProt accession to retrieve assay IDs (AIDs).

Instructions

Find PubChem bioassays associated with a biological target. Search by gene symbol (e.g. "EGFR"), protein name, NCBI Gene ID, or UniProt accession. Returns assay IDs (AIDs) which can be explored further with pubchem_get_summary.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
targetTypeYesTarget identifier type. "genesymbol" and "proteinname" accept text names. "geneid" accepts NCBI Gene IDs. "proteinaccession" accepts UniProt accessions.
targetQueryYesTarget identifier. Examples: "EGFR" (genesymbol), "Epidermal growth factor receptor" (proteinname), "1956" (geneid), "P00533" (proteinaccession).
maxResultsNoMax AIDs to return (1-200). Popular targets may have thousands of assays. Default: 50.

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
aidsYesPubChem Assay IDs.
targetTypeYesTarget identifier type used: genesymbol, proteinname, geneid, or proteinaccession.
targetQueryYesTarget identifier searched.
totalFoundYesTotal AIDs found before the maxResults cap.
truncatedNoTrue when AIDs were capped at maxResults — more assays exist than returned.
shownNoAIDs returned after the maxResults cap.
capNoThe maxResults cap that was applied.
noticeNoRecovery guidance when no assays matched — echoes the target and suggests alternative search types. Absent when assays were returned.
Behavior3/5

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

Annotations already declare readOnlyHint, idempotentHint, openWorldHint. The description adds no additional behavioral context beyond these, and does not mention rate limits or error behavior. Adequate but not enhanced.

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, no redundant information. Front-loaded with purpose. Every sentence 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?

Tool has only 3 parameters with 100% schema coverage and an output schema exists. The description covers all essential aspects: purpose, search types, return value, and next step. Complete for its complexity.

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?

Input schema has 100% coverage, but the description adds concrete examples for each parameter (e.g., 'EGFR' for genesymbol), which helps the agent understand usage. Slightly more than schema alone provides.

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 clearly states 'Find PubChem bioassays associated with a biological target' and specifies search methods (gene symbol, protein name, etc.). It distinguishes from siblings by mentioning AIDs and referencing pubchem_get_summary for further exploration.

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?

Description provides clear search methods and tells how to proceed after getting AIDs. It lacks explicit when-not-to-use or alternatives to other sibling tools, but the context is sufficient.

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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