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Wikipathways

by io.github.pipeworx-io

Search Pathways

search_pathways
Read-onlyIdempotent

Search WikiPathways (open community pathway database) for biological pathways by name. Pathways map genes/proteins/metabolites in processes like glycolysis, apoptosis, or signaling. Optionally restrict to one organism by Latin or common name. Keyless. Complements KEGG/Reactome.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
limitNoMax results (default 25, max 100).
queryYesText to match in the pathway name (case-insensitive), e.g. "glycolysis", "apoptosis".
organismNoOptional. Restrict to an organism by Latin or common name, e.g. "Homo sapiens" or "human".

TDQS

A4/5.0
Behavior4/5

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

Annotations already indicate read-only, idempotent, and non-destructive behavior. The description adds value by noting the tool is keyless, searches an open community database, and optionally restricts by organism. No contradictions.

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 very concise: four short sentences that front-load the purpose and provide essential details without wasted words. Every sentence adds value.

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?

For a search tool with 3 parameters and no output schema, the description covers the main points: purpose, database, examples, optional filter, and external context. It could briefly mention expected return format, but overall sufficient.

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%, so the baseline is 3. The description repeats parameter info (e.g., organism can be Latin or common name) but adds no new semantics beyond what the schema provides.

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 the tool searches WikiPathways for biological pathways by name, with examples like glycolysis and apoptosis. It distinguishes itself from siblings (e.g., get_pathway, list_pathways) implicitly, and mentions complementing KEGG/Reactome.

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 gives some context (keyless, complements other databases) but does not explicitly state when to use this tool versus sibling tools like get_pathway or list_pathways. Usage guidance is implied but not direct.

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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TDQS

B3.3/5.0
Disambiguation1/5

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 Consistency2/5

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.

Tool Count1/5

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.

Completeness1/5

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.

Resources