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Execute Cypher queries to retrieve biological knowledge from NASA GeneLab spaceflight experiments. Query relationships with edge properties like log2fc and p-values.

Instructions

Execute a Cypher query on the Neo4j database.

If the question is about up- or down-regulated genes, use the find_upregulated_genes or find_downreguluated genes

EDGE PROPERTIES - CRITICAL: Many relationships in this knowledge graph have properties stored as edge attributes (data ON the relationship itself). Examples include: log2fc, adj_p_value, methylation_diff, q_value, etc.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
queryYesThe Cypher query to execute.
paramsNoThe parameters to pass to the Cypher query.

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
resultYes
Behavior3/5

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

No annotations are provided, so the description carries the burden. It discloses that edge properties are on relationships and gives examples, which helps agents understand the data model. However, it does not clarify whether the tool is read-only or can modify data, nor does it mention any side effects.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness4/5

Is the description appropriately sized, front-loaded, and free of redundancy?

The description is relatively concise, with a clear main line and an important note about edge properties. There is a minor typo ('downreguluated'), but overall it is well-structured and front-loaded.

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?

Given the presence of an output schema (return values are covered) and the complexity of the tool, the description adequately highlights the critical edge property context. It could mention that it can be used for arbitrary Cypher queries, but the current content is sufficient for an informed agent.

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 coverage is 100% (both parameters described in schema). The description adds no additional meaning beyond what the schema provides for 'query' and 'params'. 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 clearly states 'Execute a Cypher query on the Neo4j database,' which is a specific verb and resource. It also distinguishes itself from sibling tools by advising when to use alternatives (find_upregulated_genes, find_downreguluated genes).

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?

The description explicitly tells when not to use this tool (for up/down-regulated genes) and mentions edge properties as critical. However, it does not provide a complete set of when-to-use guidelines or alternatives for other query types.

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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