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reactome-mcp

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by reactome

reactome_pathway_ancestors

Trace the ancestry of a Reactome pathway or reaction to see its place in the broader hierarchy.

Instructions

Get the ancestor pathway hierarchy for an event (pathway or reaction). Shows how a pathway fits into the broader Reactome structure.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
idYesReactome stable ID or database ID
Behavior3/5

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

No annotations are provided, so the description carries the full burden. It correctly implies a read-only operation ('Get') and describes the purpose, but it does not disclose output format, whether it returns just IDs or full objects, or if any special input validation applies. This is adequate for a simple read-only tool but lacks depth.

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 exactly two sentences, both front-loaded and free of filler. It delivers the essential purpose and contextual outcome without redundancy.

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?

For a tool with one parameter and no output schema, the description provides enough context for an agent to select it: it names the resource type (pathways or reactions), the relationship type (ancestors), and the use case (fitting into broader structure). It might benefit from specifying the return shape (e.g., list of ancestor IDs), but overall it's sufficiently complete for its simplicity.

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% for the single parameter 'id', which already describes it as 'Reactome stable ID or database ID'. The description adds value by clarifying that the id can refer to an 'event (pathway or reaction)', which is not explicitly stated in the schema. This extra semantic context helps the agent choose appropriate input values.

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 retrieves the 'ancestor pathway hierarchy for an event', using specific verbs and resource scope. It distinguishes from siblings like 'reactome_pathway_contained_events' (which goes downward) and 'reactome_events_hierarchy' (which may be general hierarchy) by emphasizing 'ancestors'.

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

Usage Guidelines3/5

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

The description gives clear context ('Shows how a pathway fits into the broader Reactome structure') but provides no explicit when-to-use/when-not-to-use guidance or alternatives. For example, it doesn't mention that 'reactome_events_hierarchy' might be used for differently structured queries or that this tool is for direct lineage.

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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