list_pathwaysList all WikiPathways pathways for a single organism. Give a Latin or common name, e.g. "Homo sapiens", "human", or "mouse". Returns each pathway's id, name, link, and last revision. Keyless.
| Name | Required | Description | Default |
|---|---|---|---|
| limit | No | Max results (default 50, max 200). | |
| organism | Yes | Organism by Latin or common name, e.g. "Homo sapiens", "human", "mouse". |
Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?
Annotations already provide readOnlyHint, idempotentHint, and destructiveHint, making the safety profile clear. The description adds that the tool is 'Keyless' (no authentication required) and details the return fields (id, name, link, last revision). This provides additional behavioral context beyond 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 three concise sentences with no wasted words. It front-loads the purpose and provides essential details efficiently.
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?
Despite having no output schema, the description lists the exact return fields. Combined with clear parameter info and annotations, it provides a complete picture for a simple list tool. The keyless and single-organism constraints are noted.
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 description coverage is 100%, so baseline is 3. The description adds practical examples for organism (e.g., 'Homo sapiens', 'human', 'mouse') and clarifies it accepts common names, which adds meaning beyond the schema's description.
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 'List all WikiPathways pathways for a single organism.' This is a specific verb-resource combination that distinguishes it from related tools like search_pathways, which presumably allow broader or filtered queries.
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 explains how to set the organism parameter (common or Latin names) but does not explicitly tell when to use this tool versus siblings like search_pathways or get_pathway. It implies usage for listing all pathways for an organism but lacks explicit alternatives or exclusions.
Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.
Add one secure layer between your agents and this server.
The tool set is severely mismatched: only 3 of 34 tools (get_pathway, list_pathways, search_pathways) relate to WikiPathways while the rest form overlapping Pipeworx/Polymarket families (ask_pipeworx vs ask_pipeworx_beta vs ask_pipeworx_grounded; multiple polymarket_* tools) with unclear boundaries and overlapping purposes.
Naming conventions are highly inconsistent: product-specific names (pipeworx_feedback, pipeworx_trending), generic memory verbs (remember, recall, forget), and mixed snake_case patterns with no unifying verb_noun structure. The names do not reflect the WikiPathways domain at all.
34 tools is far too many for a WikiPathways server, which only needs a handful of pathway-related operations. Nearly all tools belong to unrelated domains (SEC, FDA, Polymarket, npm, etc.), making the set feel bloated and unfocused.
For the stated WikiPathways purpose, only get, list, and search are present—no create, update, or delete operations—leaving obvious lifecycle gaps. The extensive non-WikiPathways tools do not contribute to the server's apparent domain coverage and create dead ends for agents expecting pathway management.