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Ensembl

by io.github.pipeworx-io
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Ensembl REST MCP.

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Status
Unhealthy
Uptime
37.5% over 41 days
Last Tested
Transport
Streamable HTTP
URL
Repository
pipeworx-io/mcp-ensembl
GitHub Stars
0
Server Listing
mcp-ensembl

TDQS

A3.5/5.0

Scored across 43 tools

Disambiguation1/5

Many tools have overlapping purposes, particularly the ask_pipeworx family (ask_pipeworx, ask_pipeworx_beta, ask_pipeworx_grounded) and other data-retrieval tools like deep_research, validate_claim, and suggest_questions. Company-oriented tools (entity_profile, company_facts, compare_entities, recent_changes, resolve_entity) also overlap heavily, making it difficult to select the right tool. The few genomics tools are distinct but are surrounded by unrelated financial, betting, and utility tools with unclear boundaries.

Naming Consistency2/5

Tool names are wildly inconsistent: some are descriptive phrases (ai_visibility_check, ask_pipeworx), some use underscores in compound nouns (generate_llms_txt, kalshi_weather_edge), some are single verbs (forget, recall, remember), and others are noun phrases (entity_profile, company_facts). There is no consistent verb_noun or other predictable pattern, making the naming chaotic and hard to navigate.

Tool Count2/5

With 43 tools, the count is far too high for a server named 'Ensembl' that should focus on genomics. The vast majority of tools are unrelated to that domain (finance, prediction markets, subscriptions, memory, etc.), inflating the count without serving the apparent purpose. The scope is unclear and the tool count feels bloated and unfocused.

Completeness2/5

For a server explicitly named 'Ensembl', the genomic tool surface is severely incomplete: only seven tools (lookup, lookup_symbol, sequence, variation, vep, homology, xrefs) actually serve that domain, missing core features like regulatory regions, comparative genomics, or batch queries. The remaining 36 tools are irrelevant to Ensembl, so the server fails to provide adequate coverage of its stated purpose and would cause agent failures for common Ensembl tasks.

Tool Schema Changelog

Recent tool additions, removals, and schema changes observed during successful MCP inspections.

  1. 26 tool updates
    • Changedai_visibility_check1 field changed
      • addedInput schema / examples
        Added value: +[
+  {
+    "entity": "Tesla"
+  }
+]
    • Changedask_pipeworx_beta1 field changed
      • addedInput schema / examples
        Added value: +[
+  {
+    "question": "What is the current US unemployment rate?"
+  }
+]
    • Changedask_pipeworx_grounded1 field changed
      • addedInput schema / examples
        Added value: +[
+  {
+    "question": "What was Apple's fiscal 2023 revenue?"
+  }
+]
    • Addedcompany_facts
    • Changedcompare_entities1 field changed
      • addedInput schema / examples
        Added value: +[
+  {
+    "type": "company",
+    "values": [
+      "AAPL",
+      "MSFT"
+    ]
+  }
+]
    • Changeddeep_research1 field changed
      • addedInput schema / examples
        Added value: +[
+  {
+    "depth": "quick",
+    "question": "What is the current US unemployment rate and how has it changed over the past year?"
+  }
+]
    • Changedentity_profile1 field changed
      • addedInput schema / examples
        Added value: +[
+  {
+    "type": "company",
+    "value": "AAPL"
+  }
+]
    • Changedgenerate_llms_txt1 field changed
      • addedInput schema / examples
        Added value: +[
+  {
+    "url": "https://pipeworx.io"
+  }
+]
    • Addedkalshi_weather_edge
    • Changedpipeworx_feedback1 field changed
      • addedInput schema / examples
        Added value: +[
+  {
+    "message": "Fleet #2184 smoke test: verifying pipeworx_feedback example call returns non-empty.",
+    "type": "other"
+  }
+]
    • Changedpipeworx_trending1 field changed
      • addedInput schema / examples
        Added value: +[
+  {
+    "window": "7d"
+  }
+]
    • Changedpolymarket_arbitrage1 field changed
      • addedInput schema / examples
        Added value: +[
+  {
+    "topic": "Fed rate decision"
+  }
+]
    • Changedpolymarket_edge_tracker1 field changed
      • addedInput schema / examples
        Added value: +[
+  {
+    "days": 14,
+    "window": "1wk"
+  }
+]
    • Changedpolymarket_edges3 fields changed
      • addedInput schema / examples
        Added value: +[
+  {
+    "limit": 5,
+    "window": "1wk"
+  }
+]
      • changedInput schema / properties / min_edge_pp / description
        Previous value: -"Minimum |edge| in percentage points to include (default 0.5). Edge is evaluated NET of slippage."New value: +"Minimum |edge| in percentage points to include (default 0.5). Edge is evaluated NET of slippage and Polymarket's own taker fee."
      • changedInput schema / properties / slippage_pp / description
        Previous value: -"Assumed execution slippage in percentage points per leg (default 0.3). Subtracted from raw |edge| before ranking and Kelly sizing. Polymarket has zero trading fees as of 2024 but bid/ask + thin depth typically eats 20-50bp per trade. Bump for very thin partitions; drop to 0 if you have a smarter fill model."New value: +"Assumed execution slippage in percentage points per leg (default 0.3), for bid/ask + thin depth cost that a last-trade price does not show. Subtracted from raw |edge| before ranking and Kelly sizing, ON TOP OF Polymarket's own taker fee — which is NOT zero (rate 0.04-0.07 depending on category, read off each market's own published fee schedule; see fees_pp_applied on every row and fees.ts for the full schedule). Bump slippage for very thin partitions; drop to 0 if you have a smarter fill model — the fee still applies regardless."
    • Changedpolymarket_fill_risk1 field changed
      • addedInput schema / examples
        Added value: +[
+  {
+    "market": "will-the-fed-increase-interest-rates-by-25-bps-after-the-december-2026-meeting-20260729232808636",
+    "side": "buy_yes",
+    "size_usd": 1000
+  }
+]
    • Changedrecent_changes1 field changed
      • addedInput schema / examples
        Added value: +[
+  {
+    "since": "30d",
+    "type": "company",
+    "value": "AAPL"
+  }
+]
    • Addedrelease_calendar_markets
    • Changedremember1 field changed
      • addedInput schema / examples
        Added value: +[
+  {
+    "key": "target_ticker",
+    "value": "AAPL"
+  }
+]
    • Addedresolution_audit
    • Addedresolution_diff
    • Changedresolve_entity1 field changed
      • addedInput schema / examples
        Added value: +[
+  {
+    "type": "company",
+    "value": "AAPL"
+  }
+]
    • Changedscan_competitor_ai_presence1 field changed
      • addedInput schema / examples
        Added value: +[
+  {
+    "entities": [
+      "Pipeworx",
+      "Zapier"
+    ]
+  }
+]
    • Changedscan_dependency1 field changed
      • addedInput schema / examples
        Added value: +[
+  {
+    "package": "left-pad"
+  }
+]
    • Changedsearch_within1 field changed
      • addedInput schema / examples
        Added value: +[
+  {
+    "query": "supply-chain risk",
+    "text": "Apple Inc. reported fiscal 2023 revenue of $383.285 billion, driven by strong iPhone and Services growth. Net income was $96.995 billion. The company faced supply-chain risk in China during the quarter."
+  }
+]
    • Changedsuggest_questions1 field changed
      • addedInput schema / examples
        Added value: +[
+  {
+    "topic": "finance"
+  }
+]
    • Changedvalidate_claim1 field changed
      • addedInput schema / examples
        Added value: +[
+  {
+    "claim": "Apple's fiscal 2023 revenue was $383 billion"
+  }
+]
  2. 1 tool update
    • Changedbet_research2 fields changed
      • changedInput schema / examples
        Previous value: -[
-  {
-    "market": "when-will-bitcoin-hit-150k"
-  },
-  {
-    "market": "https://polymarket.com/event/when-will-bitcoin-hit-150k"
-  }
-]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"
+  }
+]
      • changedInput schema / properties / market / description
        Previous value: -"Polymarket slug (\"when-will-bitcoin-hit-150k\"), 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."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."
  3. 2 tool updates
    • Changedbet_research2 fields changed
      • changedInput schema / examples
        Previous 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": "when-will-bitcoin-hit-150k"
+  },
+  {
+    "market": "https://polymarket.com/event/when-will-bitcoin-hit-150k"
+  }
+]
      • changedInput schema / properties / market / description
        Previous 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 (\"when-will-bitcoin-hit-150k\"), 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."
    • Changedpolymarket_kalshi_spread2 fields changed
      • changedInput schema / examples
        Previous value: -[
-  {
-    "topic": "fed"
-  },
-  {
-    "topic": "btc"
-  }
-]New value: +[
+  {
+    "topic": "fed"
+  },
+  {
+    "topic": "btc"
+  },
+  {
+    "topic": "bitcoin"
+  },
+  {
+    "topic": "fed rate decision"
+  }
+]
      • changedInput schema / properties / topic / description
        Previous 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."
  4. 1 tool update
    • Changedvep4 fields changed
      • changedInput schema / examples
        Previous value: -[
-  {
-    "allele": "C",
-    "region": "9:22125504-22125504:1",
-    "species": "human"
-  },
-  {
-    "allele": "A",
-    "assembly": "GRCh37",
-    "region": "1:11856378-11856378:1",
-    "species": "human"
-  }
-]New value: +[
+  {
+    "allele": "C",
+    "assembly": "GRCh38",
+    "region": "9:22125504-22125504:1",
+    "species": "human"
+  },
+  {
+    "allele": "A",
+    "assembly": "GRCh37",
+    "region": "1:11856378-11856378:1",
+    "species": "human"
+  }
+]
      • changedInput schema / properties / assembly / description
        Previous value: -"Human genome build: \"GRCh38\" (the default) or \"GRCh37\" (= hg19). Coordinates you pass and coordinates you get back are both in this build. Older variant lists, spreadsheets and published tables are usually GRCh37."New value: +"REQUIRED. The genome build your region is in: \"GRCh38\" (= hg38) or \"GRCh37\" (= hg19). There is no default on purpose — a genomic position is valid in BOTH builds, so an unstated build cannot be detected, only guessed wrong, and a wrong guess returns confident consequence calls for a different gene instead of an error."
      • changedInput schema / properties / region / description
        Previous value: -"e.g. \"9:22125504-22125504:1\" — in the build named by assembly (GRCh38 by default)."New value: +"e.g. \"9:22125504-22125504:1\" — in the build named by assembly."
      • changedInput schema / required
        Previous value: -[
-  "species",
-  "region",
-  "allele"
-]New value: +[
+  "species",
+  "region",
+  "allele",
+  "assembly"
+]
  5. 5 tool updates
    • Changedlookup1 field changed
      • addedInput schema / properties / assembly
        Added value: +{
+  "description": "Human genome build: \"GRCh38\" (the default) or \"GRCh37\" (= hg19). Coordinates you pass and coordinates you get back are both in this build. Older variant lists, spreadsheets and published tables are usually GRCh37.",
+  "type": "string"
+}
    • Changedlookup_symbol1 field changed
      • addedInput schema / properties / assembly
        Added value: +{
+  "description": "Human genome build: \"GRCh38\" (the default) or \"GRCh37\" (= hg19). Coordinates you pass and coordinates you get back are both in this build. Older variant lists, spreadsheets and published tables are usually GRCh37.",
+  "type": "string"
+}
    • Changedsequence1 field changed
      • addedInput schema / properties / assembly
        Added value: +{
+  "description": "Human genome build: \"GRCh38\" (the default) or \"GRCh37\" (= hg19). Coordinates you pass and coordinates you get back are both in this build. Older variant lists, spreadsheets and published tables are usually GRCh37.",
+  "type": "string"
+}
    • Changedvariation1 field changed
      • addedInput schema / properties / assembly
        Added value: +{
+  "description": "Human genome build: \"GRCh38\" (the default) or \"GRCh37\" (= hg19). Coordinates you pass and coordinates you get back are both in this build. Older variant lists, spreadsheets and published tables are usually GRCh37.",
+  "type": "string"
+}
    • Changedvep3 fields changed
      • changedInput schema / examples
        Previous value: -[
-  {
-    "allele": "C",
-    "region": "9:22125504-22125504:1",
-    "species": "human"
-  }
-]New value: +[
+  {
+    "allele": "C",
+    "region": "9:22125504-22125504:1",
+    "species": "human"
+  },
+  {
+    "allele": "A",
+    "assembly": "GRCh37",
+    "region": "1:11856378-11856378:1",
+    "species": "human"
+  }
+]
      • addedInput schema / properties / assembly
        Added value: +{
+  "description": "Human genome build: \"GRCh38\" (the default) or \"GRCh37\" (= hg19). Coordinates you pass and coordinates you get back are both in this build. Older variant lists, spreadsheets and published tables are usually GRCh37.",
+  "type": "string"
+}
      • changedInput schema / properties / region / description
        Previous value: -"e.g. \"9:22125504-22125504:1\""New value: +"e.g. \"9:22125504-22125504:1\" — in the build named by assembly (GRCh38 by default)."

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