WikiPathways MCP — open community pathway database.
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Scored across 34 tools
Multiple tools have unclear boundaries: ask_pipeworx, ask_pipeworx_beta (explicitly 'currently matches ask_pipeworx exactly'), ask_pipeworx_grounded, and deep_research all route the same kinds of questions, and the polymarket family (edges, arbitrage, edge_tracker, fill_risk, kalshi_spread, bet_research) heavily overlaps in purpose. Descriptions are verbose but the boundaries between 'which router' and 'which betting tool' remain ambiguous.
Nearly all tools use snake_case with a predictable verb_noun or noun_noun pattern (list_pathways, get_pathway, search_pathways, compare_entities, resolve_entity, polymarket_*). Minor deviations like bare-verb 'forget'/'recall' and noun-first 'entity_profile'/'bet_research' break the pattern slightly but the convention is largely consistent.
34 tools is heavy for the stated 'Wikipathways' scope, which only needs about three pathway tools. The vast majority of the surface belongs to an unrelated data-routing/betting platform, so the count is both large and mismatched to the server's apparent purpose.
For the WikiPathways domain the surface only covers search/list/get-metadata, missing pathway content, gene/protein membership, and downloads, while the bulk of tools serve an entirely different platform. This leaves the pathway workflow with dead ends and the overall set incoherent relative to the server name.
Recent tool additions, removals, and schema changes observed during successful MCP inspections.
bet_research2 fields changedInput schema / examplesPrevious value: -[
- {
- "market": "will-bitcoin-reach-100k-in-july-2026"
- },
- {
- "market": "https://polymarket.com/event/will-bitcoin-hit-150k-by-june-30-2026"
- }
-]New value: +[
+ {
+ "market": "will-kristi-noem-win-the-2028-republican-presidential-nomination"
+ },
+ {
+ "market": "https://polymarket.com/event/will-kristi-noem-win-the-2028-republican-presidential-nomination"
+ }
+]Input schema / properties / market / descriptionPrevious value: -"Polymarket slug (\"will-bitcoin-hit-150k-by-june-30-2026\"), full URL (\"https://polymarket.com/event/...\"), or question text (\"Will Bitcoin hit $150k by June 30?\")"New value: +"Polymarket slug (\"will-kristi-noem-win-the-2028-republican-presidential-nomination\"), full URL (\"https://polymarket.com/event/...\"), or question text (\"Will Bitcoin hit $150k?\"). Dated slugs stop resolving once they settle — Polymarket de-indexes resolved markets — so prefer an undated one."polymarket_kalshi_spread2 fields changedInput schema / examplesPrevious value: -[
- {
- "topic": "fed"
- },
- {
- "topic": "btc"
- }
-]New value: +[
+ {
+ "topic": "fed"
+ },
+ {
+ "topic": "btc"
+ },
+ {
+ "topic": "bitcoin"
+ },
+ {
+ "topic": "fed rate decision"
+ }
+]Input schema / properties / topic / descriptionPrevious value: -"Pre-mapped: fed | btc | cpi | gdp | sp500 | recession | next_pope | next_uk_pm | next_israel_pm | 2028_president"New value: +"Subject to compare. Canonical keys: fed | btc | eth | cpi | gdp | sp500 | recession | next_pope | next_uk_pm | next_israel_pm | 2028_president — but aliases and keywords resolve too (\"bitcoin\", \"fed rate decision\", \"ethereum\", \"inflation\", \"s&p 500\", \"us recession\", \"next pope\", \"2028 election\"). Check resolution.topic_matched_by in the response: \"exact\"/\"alias\" is a curated pairing, \"phrase\"/\"token\" is a keyword guess."cBioPortal MCP — cancer genomics portal.
Open Targets MCP — disease/target/drug knowledge graph.
MetaboLights MCP — EBI's metabolomics study repository.
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