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tc2fh
by tc2fh

get_event_sbml

Export Reactome pathways or reactions to SBML or SBGN formats, with automatic truncation for large files.

Instructions

Export a pathway/reaction to SBML or SBGN, inline with size guarding.

SBML connects Reactome straight into systems-biology tooling (and the
BioModels workflow). Large exports are head/tail truncated with a pointer
to `download_export` so multi-MB XML never floods the chat.

Args:
    stable_id: Event stable id, e.g. "R-HSA-69620".
    fmt: "sbml" (default) or "sbgn".
    max_chars: Max characters to return inline (default 50000).

Returns:
    Dict with `stId`, `format`, `mimeType`, `total_chars`, `truncated`, and
    either `content` (full text) or `content_head` + `content_tail` +
    `note` when truncated.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
fmtNosbml
max_charsNo
stable_idYes
Behavior5/5

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

With no annotations, the description carries the full burden. It discloses truncation behavior, return format, and the safety guarantee that multi-MB XML never floods the chat. This is thorough and transparent.

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, front-loaded with a clear summary, followed by a brief rationale and then concise parameter and return details. Every sentence adds value; no redundancy or filler.

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 the tool's moderate complexity and lack of output schema, the description is complete. It covers the full return structure, truncation behavior, and the relationship to `download_export`, leaving no major gaps for invocation.

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?

The schema provides zero parameter descriptions, and the description fully compensates. Each parameter (`stable_id`, `fmt`, `max_chars`) is explained with examples, defaults, and semantics, far exceeding what the schema alone offers.

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 the tool exports a pathway/reaction to SBML or SBGN, with a specific verb and resource. It distinguishes itself from the sibling tool `download_export` by explicitly mentioning size guarding and truncation, making its scope unambiguous.

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?

It explains when to use this tool (inline export for systems biology) and explicitly points to `download_export` for large exports that exceed inline limits. This provides an explicit alternative and contextualizes usage.

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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