PlantCyc: Metabolic Pathways

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

Beyond annotations (readOnlyHint, idempotentHint, etc.), the description adds that the tool walks gene→enzyme→catalyzed reactions→pathways, returns found=false for non-enzymatic genes without error, caps lists but reports true totals via reaction_count/pathway_count, and details response structure (enzymes[], reactions[], pathways[]). No contradiction with annotations.

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 well-structured with front-loaded purpose, followed by walkthrough, special cases, count behavior, and supported organisms. Every sentence adds value, though it is somewhat lengthy. No redundancy.

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 presence of annotations and an output schema, the description provides all necessary information: purpose, input parameters with extra context, behavioral details (non-enzymatic handling, capped lists, true totals), supported organisms, and contrast with other resources. It is complete for an agent to select and invoke correctly.

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?

Schema coverage is 100%, but the description adds significant meaning: for 'organism', it specifies accepted formats (slug, scientific/common name, NCBI taxid) and lists the 11 supported organisms; for 'locus', it provides examples (AT3G51240, Os11g0530600). Default organism is stated. This goes beyond the schema alone.

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 fetches metabolic annotations for a locus from PlantCyc, specifying the walkthrough from gene to enzyme to reactions to pathways. It explicitly distinguishes itself from KEGG and GO, and lists supported organisms and the default. The verb 'fetch' with the resource 'metabolic annotation for a locus' is specific.

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?

The description indicates when to use (to get metabolic-pathway view not provided by KEGG/GO) and which organisms are supported (listing 11, noting wheat is not mapped). It also explains behavior for non-enzymatic genes. However, it does not explicitly mention when not to use or directly contrast with siblings like kegg_pathways, though the differentiation is implied.

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