AGR MCP Server

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

No annotations are provided, so the description carries full burden. It states the tool finds orthologs and returns homologs from all Alliance model organisms, which gives some behavioral context (e.g., cross-species focus, data source). However, it lacks details on permissions, rate limits, error handling, or what 'orthologous genes' entails operationally (e.g., algorithm, confidence thresholds). For a tool with no annotations, this is insufficient, scoring 2.

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

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

The description is two concise sentences that efficiently convey the tool's function and scope without waste. It is front-loaded with the core purpose and adds necessary context about the data source. Every sentence earns its place, making it appropriately sized and well-structured.

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

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

Given the tool's moderate complexity (finding orthologs across species), no annotations, no output schema, and 1 parameter with full schema coverage, the description is partially complete. It covers what the tool does and the data source but lacks details on output format, behavioral traits, or usage context. This makes it adequate but with clear gaps, scoring 3 as the minimum viable.

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

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

The input schema has 1 parameter with 100% description coverage ('Gene identifier'), so the schema does the heavy lifting. The description adds no additional parameter semantics beyond implying the gene_id is used to find orthologs. According to rules, with high schema coverage (>80%), the baseline is 3 even with no param info in the description, which applies here.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Does the description clearly state what the tool does and how it differs from similar tools?

The description clearly states the tool's purpose: 'Find orthologous genes across species' specifies the action and resource. It distinguishes from siblings like get_gene_info or search_genes by focusing on cross-species homology rather than gene-specific data or general search. However, it doesn't explicitly differentiate from potential overlap with other homology tools not listed, keeping it at 4 rather than 5.

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

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

No explicit guidance on when to use this tool versus alternatives is provided. The description mentions 'Returns homologs from all Alliance model organisms,' which implies a broad scope but doesn't specify when to choose this over sibling tools like get_gene_info for single-species data or search_genes for queries. Without clear when/when-not instructions or named alternatives, it scores 2.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.