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reactome-mcp

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by reactome

reactome_complexes_containing

Discover all Reactome complexes containing a specific external identifier (like a UniProt ID) to understand their role in biological pathways.

Instructions

Find all Reactome complexes that contain a specific external identifier (e.g., UniProt ID).

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
resourceYesDatabase name (e.g., 'UniProt', 'ChEBI', 'Ensembl')
identifierYesExternal identifier (e.g., 'P04637' for UniProt)
Behavior2/5

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

No annotations are provided, so the description carries the full burden of behavioral disclosure. It only states 'Find all' which implies a read operation returning a collection of complexes, but it does not disclose potential limitations, pagination, output format, or any edge cases (e.g., how partial matches are handled). This is a minimal description that fails to add behavioral context beyond the basic action.

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 a single, front-loaded sentence that immediately communicates the core purpose. Every word is useful, with no fluff or repetition. It is appropriately concise for the tool's simplicity.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness3/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

For a simple lookup tool with two fully documented parameters, the description is adequate to convey what the tool does. However, with no output schema and no annotations, it leaves the return format and any usage caveats unexplained. It also does not position the tool among its many siblings, so the context is not fully complete. This is not severely deficient but has clear gaps.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters3/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

Schema description coverage is 100%, with both 'resource' and 'identifier' already explained (e.g., UniProt, ChEBI, Ensembl for resource; P04637 for identifier). The description largely repeats these examples ('e.g., UniProt ID') without adding new semantic meaning. It does not explain how resource and identifier interact or any validation rules, so it adds no value beyond the 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?

The description clearly states the tool's action ('Find all Reactome complexes'), the resource (Reactome complexes), and the specific scope (containing a specific external identifier). This is a specific verb+resource+scope combination that distinguishes it from sibling tools like reactome_complex_subunits (which returns subunits of a given complex) and reactome_entity_component_of (which finds components of an entity). The example (UniProt ID) further clarifies the input type.

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 implies when to use it: when you have an external identifier and need complexes containing it. However, it provides no explicit guidance on when not to use it or how it differs from alternatives such as reactome_entity_component_of or reactome_reference_entities. There are no exclusions or alternative tool mentions, so it stops at implied usage rather than explicit guidance.

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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