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tc2fh
by tc2fh

get_analysis_results

Retrieve paginated, sortable results of a prior Reactome pathway analysis using its token, with optional species and p-value filters.

Instructions

Retrieve (page/sort/filter) the results of a prior analysis by token.

Args:
    token: The `token` returned by `analyze_identifiers`.
    species: Optional species filter.
    sort_by: Sort key (e.g. ENTITIES_PVALUE, ENTITIES_FDR).
    p_value: Keep pathways with entity p-value <= this.
    page: 1-based page number.
    page_size: Pathways per page.
    resource: Identifier resource to score against (default "TOTAL").

Returns:
    Same shape as `analyze_identifiers`.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
pageNo
tokenYes
p_valueNo
sort_byNoENTITIES_PVALUE
speciesNo
resourceNoTOTAL
page_sizeNo
Behavior4/5

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

No annotations are provided, so the description must carry the behavioral burden. It does so with a non-destructive verb ('Retrieve'), explicit paging/sorting/filtering behavior, and a note that the return shape matches analyze_identifiers. It doesn't mention edge cases like token expiration or error handling, but for a read-only retrieval tool this is sufficient.

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?

The description is well-structured with a one-sentence summary followed by a compact Args and Returns list. Every sentence adds value, and there is no redundant repetition of schema information.

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?

All parameters are described, and the return shape is addressed via cross-reference to analyze_identifiers. However, it relies on the agent already knowing analyze_identifiers' return schema and doesn't mention potential error states or result availability, which is a minor gap for such a parameter-rich tool.

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 coverage is 0%, so the description fully compensates by explaining all 7 parameters with meaningful detail, including concrete examples for sort_by (ENTITIES_PVALUE, ENTITIES_FDR) and the exact meaning of p_value. This is far more useful than the bare schema titles and defaults.

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 begins with a clear verb ('Retrieve') and names the resource ('results of a prior analysis'), with an explicit dependency on the token from analyze_identifiers. The parenthetical '(page/sort/filter)' conveys the tool's scope, which helps distinguish it from the many sibling tools.

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?

It clearly establishes when to use this tool: after a prior analysis has been performed, with a token returned by analyze_identifiers. It doesn't explicitly list alternative tools or when not to use it, but the context is unambiguous and no alternatives are truly competing for this exact task.

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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