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Search Assays

pubchem_search_assays
Read-onlyIdempotent

Retrieve PubChem bioassay IDs for a biological target. Search using gene symbol, protein name, NCBI Gene ID, or UniProt accession to get a page of 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 a page of assay IDs (AIDs) — page past maxResults with offset — which can be explored further with pubchem_get_summary.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
offsetNoZero-based index of the first AID to return. Pass the nextOffset from a previous call to read the following page. Default: 0.
maxResultsNoMax AIDs to return per page (1-200). Popular targets may have thousands of assays; use offset to reach the ones past this page. Default: 50.
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).

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
capNoThe maxResults cap that was applied.
aidsYesPubChem Assay IDs.
shownNoAIDs returned on this page.
noticeNoRecovery guidance when no assays matched, when the offset runs past the result set, or when further pages remain. Absent when this page is complete and non-empty.
offsetYesZero-based index of the first AID returned.
truncatedNoTrue when matching AIDs remain past this page.
nextOffsetNoOffset to pass on the next call to continue past this page. Omitted when no further AIDs match.
targetTypeYesTarget identifier type used: genesymbol, proteinname, geneid, or proteinaccession.
totalFoundYesTotal AIDs found for this target, across all pages.
targetQueryYesTarget identifier searched.
Behavior3/5

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

Annotations already declare readOnlyHint, idempotentHint, openWorldHint, so the description's behavioral disclosure is minimal. It adds that results are a page of AIDs and describes pagination, which is useful but not required beyond 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 with no filler. Key information is front-loaded: purpose, search methods, return type, pagination, and follow-up tool.

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 presence of output schema, the description covers search scope, pagination, and next steps. It is complete for a search tool with no missing gaps.

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%, so baseline is 3. The description adds value by explaining the purpose of the return (AIDs), how pagination works (page past maxResults with offset), and the relationship between targetType and targetQuery examples. This enhances understanding 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?

Clearly states it finds PubChem bioassays associated with biological targets, listing specific search types (gene symbol, protein name, NCBI Gene ID, UniProt accession). This distinguishes it from sibling tools like pubchem_search_compounds.

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?

Explains pagination using offset and maxResults, and suggests exploring results further with pubchem_get_summary. Does not explicitly provide when-not or alternatives, but context is sufficient for a search tool.

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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