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reactome-mcp

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by reactome

reactome_analysis_found_entities

Retrieve identifiers found in a pathway from a Reactome analysis result using the analysis token and pathway ID.

Instructions

Get the identifiers that were found in a specific pathway from an analysis result.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
tokenYesAnalysis token
pathwayYesPathway stable ID (e.g., R-HSA-109582)
resourceNoResource filter (TOTAL, UNIPROT, ENSEMBL, etc.)TOTAL
Behavior2/5

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

No annotations are provided, so the description carries the burden of disclosing behavioral traits. It only states 'Get the identifiers' without mentioning output format, pagination, resource filtering behavior, or any side effects. The read-only nature is implied by 'Get' but not explicitly stated, and no other behavioral details are given.

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, concise sentence that immediately states the action and target. It contains no filler or repetition, and the structure is front-loaded with the core purpose.

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 retrieval tool with fully described parameters, the description is minimally viable but lacks some context: it does not explain the return format, specify that it is read-only, or provide guidance on when to use this versus related tools. Given no output schema and no annotations, the description could benefit from a bit more detail, but it is not severely incomplete.

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?

The schema descriptions fully cover all three parameters (token, pathway, resource) with clear meanings, achieving 100% schema description coverage. The tool description itself adds no additional parameter semantics beyond what the schema already provides, so the baseline score of 3 is appropriate.

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 uses a specific verb 'Get' and resource 'identifiers that were found in a specific pathway from an analysis result', clearly distinguishing this from the sibling tool reactome_analysis_not_found (which presumably returns not-found identifiers). The wording is precise and unambiguous.

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 usage context: it requires an analysis token and a specific pathway, and is for retrieving found identifiers. However, it does not explicitly state when to use this tool versus alternatives like reactome_analysis_not_found, nor does it provide any exclusions or prerequisite conditions beyond the implied need for a prior analysis.

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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