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Gnomad

by io.github.pipeworx-io
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gnomAD MCP — Broad Institute Genome Aggregation Database (GraphQL).

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Status
Unhealthy
Uptime
28.9% over 61 days
Last Tested
Transport
Streamable HTTP
URL
Repository
pipeworx-io/mcp-gnomad
GitHub Stars
0
Server Listing
mcp-gnomad

TDQS

A3.6/5.0

Scored across 41 tools

Disambiguation2/5

Several clusters overlap heavily: ask_pipeworx/ask_pipeworx_beta/ask_pipeworx_grounded/deep_research/validate_claim all answer questions; polymarket_edges/polymarket_arbitrage/polymarket_fill_risk/polymarket_kalshi_spread/kalshi_weather_edge all scan for edge; ai_visibility_check and scan_competitor_ai_presence both score AI visibility. The descriptions provide guidance, but an agent must read carefully to avoid choosing the wrong variant or covered-uncovered route.

Naming Consistency3/5

All names use snake_case, which is consistent, but the structural pattern is mixed: bare nouns (gene, region, variant, transcript), prefixed meta-tools (ask_pipeworx_*, polymarket_*), and verb_noun tools (validate_claim, compare_entities, discover_tools). It remains readable, with no camelCase chaos, but the naming is not a predictable verb_noun pattern.

Tool Count2/5

41 tools is heavy for a single server, especially one named Gnomad whose actual gnomAD surface is only a handful of tools. The set also spans unrelated domains like prediction markets, SEC financials, AI visibility, package dependency checks, memory, and subscriptions, so many tools do not obviously earn their place in one coherent toolkit.

Completeness3/5

For gnomAD lookups there are core operations: search, gene, region, variant, and transcript, which cover the main retrieval paths. However, there is no explicit gene-constraint or coverage endpoint, and the broader cross-domain surface is fragmented, with notable gaps that agents must work around using meta-tools like ask_pipeworx or deep_research.

Tool Schema Changelog

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

  1. 8 tool updates
    • Changedask_pipeworx3 fields changed
      • addedInput schema / properties / ask
        Added value: +{
+  "description": "Alias for question.",
+  "type": "string"
+}
      • addedInput schema / properties / message
        Added value: +{
+  "description": "Alias for question.",
+  "type": "string"
+}
      • changedInput schema / properties / question / description
        Previous value: -"Your question or request in natural language. Accepts query, q, prompt, text, input as aliases."New value: +"Your question or request in natural language. Accepts query, q, prompt, text, input, ask, message as aliases."
    • Changedask_pipeworx_beta3 fields changed
      • addedInput schema / properties / ask
        Added value: +{
+  "description": "Alias for question.",
+  "type": "string"
+}
      • addedInput schema / properties / message
        Added value: +{
+  "description": "Alias for question.",
+  "type": "string"
+}
      • changedInput schema / properties / question / description
        Previous value: -"Your question or request in natural language. Accepts query, q, prompt, text, input as aliases."New value: +"Your question or request in natural language. Accepts query, q, prompt, text, input, ask, message as aliases."
    • Changedask_pipeworx_grounded3 fields changed
      • addedInput schema / properties / ask
        Added value: +{
+  "description": "Alias for question.",
+  "type": "string"
+}
      • addedInput schema / properties / message
        Added value: +{
+  "description": "Alias for question.",
+  "type": "string"
+}
      • changedInput schema / properties / question / description
        Previous value: -"Your question in natural language. Accepts query, q, prompt, text, input as aliases."New value: +"Your question in natural language. Accepts query, q, prompt, text, input, ask, message as aliases."
    • Changeddeep_research8 fields changed
      • addedInput schema / properties / ask
        Added value: +{
+  "description": "Alias for question.",
+  "type": "string"
+}
      • addedInput schema / properties / input
        Added value: +{
+  "description": "Alias for question.",
+  "type": "string"
+}
      • addedInput schema / properties / message
        Added value: +{
+  "description": "Alias for question.",
+  "type": "string"
+}
      • addedInput schema / properties / prompt
        Added value: +{
+  "description": "Alias for question.",
+  "type": "string"
+}
      • addedInput schema / properties / q
        Added value: +{
+  "description": "Alias for question.",
+  "type": "string"
+}
      • addedInput schema / properties / query
        Added value: +{
+  "description": "Alias for question.",
+  "type": "string"
+}
      • changedInput schema / properties / question / description
        Previous value: -"The research question, in natural language. Broad/multi-part is fine — decomposition is the point."New value: +"The research question, in natural language. Broad/multi-part is fine — decomposition is the point. Accepts query, q, prompt, text, input, ask, message as aliases."
      • addedInput schema / properties / text
        Added value: +{
+  "description": "Alias for question.",
+  "type": "string"
+}
    • Changedforget4 fields changed
      • addedInput schema / properties / k
        Added value: +{
+  "description": "Alias for key.",
+  "type": "string"
+}
      • changedInput schema / properties / key / description
        Previous value: -"Memory key to delete"New value: +"Memory key to delete. Accepts name, k, label as aliases."
      • addedInput schema / properties / label
        Added value: +{
+  "description": "Alias for key.",
+  "type": "string"
+}
      • addedInput schema / properties / name
        Added value: +{
+  "description": "Alias for key.",
+  "type": "string"
+}
    • Changedrecall4 fields changed
      • addedInput schema / properties / k
        Added value: +{
+  "description": "Alias for key.",
+  "type": "string"
+}
      • changedInput schema / properties / key / description
        Previous value: -"Memory key to retrieve (omit to list all keys)"New value: +"Memory key to retrieve (omit to list all keys). Accepts name, k, label as aliases."
      • addedInput schema / properties / label
        Added value: +{
+  "description": "Alias for key.",
+  "type": "string"
+}
      • addedInput schema / properties / name
        Added value: +{
+  "description": "Alias for key.",
+  "type": "string"
+}
    • Changedrelease_calendar_markets2 fields changed
      • addedOutput schema / properties / empty_reason
        Added value: +{
+  "description": "Present ONLY on a zero-release window: \"no_releases_in_window\". The window was queried and nothing is scheduled — this is an answer, not a failure.",
+  "type": "string"
+}
      • addedOutput schema / properties / hint
        Added value: +{
+  "description": "Present ONLY on a zero-release window: what to change (usually a wider `hours`).",
+  "type": "string"
+}
    • Changedremember9 fields changed
      • addedInput schema / properties / content
        Added value: +{
+  "description": "Alias for value.",
+  "type": "string"
+}
      • addedInput schema / properties / data
        Added value: +{
+  "description": "Alias for value.",
+  "type": "string"
+}
      • addedInput schema / properties / k
        Added value: +{
+  "description": "Alias for key.",
+  "type": "string"
+}
      • changedInput schema / properties / key / description
        Previous value: -"Memory key (e.g., \"subject_property\", \"target_ticker\", \"user_preference\")"New value: +"Memory key (e.g., \"subject_property\", \"target_ticker\", \"user_preference\"). Accepts name, k, label as aliases."
      • addedInput schema / properties / label
        Added value: +{
+  "description": "Alias for key.",
+  "type": "string"
+}
      • addedInput schema / properties / name
        Added value: +{
+  "description": "Alias for key.",
+  "type": "string"
+}
      • addedInput schema / properties / text
        Added value: +{
+  "description": "Alias for value.",
+  "type": "string"
+}
      • addedInput schema / properties / v
        Added value: +{
+  "description": "Alias for value.",
+  "type": "string"
+}
      • changedInput schema / properties / value / description
        Previous value: -"Value to store (any text — findings, addresses, preferences, notes)"New value: +"Value to store (any text — findings, addresses, preferences, notes). Accepts content, text, data, v as aliases; a non-string value is stored as JSON."
  2. 22 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?"
+  }
+]
    • Changedcompany_facts5 fields changed
      • addedInput schema / examples
        Added value: +[
+  {
+    "attribute": "revenue",
+    "company": "AAPL",
+    "period": {
+      "fiscal_year": 2023,
+      "type": "annual"
+    }
+  }
+]
      • addedInput schema / properties / as_of
        Added value: +{
+  "description": "Past ISO timestamp with timezone. Replay the latest answer actually recorded by that instant; no invented history or live fallback.",
+  "type": "string"
+}
      • addedInput schema / properties / exclude_publishers
        Added value: +{
+  "description": "Publisher ids forbidden for fact retrieval: sec, fmp, alphavantage. Case and surrounding whitespace are normalized; unknown ids are refused. Excluding sec currently leaves no eligible fact source and returns unavailable/sources_excluded with the selection reasons. Identity and fiscal-calendar lookups may still use SEC; no excluded financial concept is fetched.",
+  "items": {
+    "type": "string"
+  },
+  "type": "array"
+}
      • addedInput schema / properties / freshness
        Added value: +{
+  "description": "cached (default) permits an eligible stored answer; fresh requires an upstream refresh and never silently falls back to stale data.",
+  "enum": [
+    "cached",
+    "fresh"
+  ],
+  "type": "string"
+}
      • addedInput schema / properties / max_age
        Added value: +{
+  "description": "Maximum age in seconds of the upstream publication, not our fetch. Older or undated facts are withheld.",
+  "maximum": 3155760000,
+  "minimum": 0,
+  "type": "number"
+}
    • 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"
+  }
+]
    • 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"
+  }
+]
    • Changedremember1 field changed
      • addedInput schema / examples
        Added value: +[
+  {
+    "key": "target_ticker",
+    "value": "AAPL"
+  }
+]
    • 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"
+  }
+]
  3. 8 tool updates
    • Addedcompany_facts
    • Changedgene3 fields changed
      • changedOutput schema / properties / gene / properties / variants / items / properties / exome / type
        Previous value: -"object"New value: +[
+  "object",
+  "null"
+]
      • changedOutput schema / properties / gene / properties / variants / items / properties / genome / type
        Previous value: -"object"New value: +[
+  "object",
+  "null"
+]
      • changedOutput schema / properties / gene / properties / variants / items / properties / hgvsp / type
        Previous value: -"string"New value: +[
+  "string",
+  "null"
+]
    • Addedkalshi_weather_edge
    • Changedregion1 field changed
      • changedOutput schema / properties / region / properties / variants / items / properties / exome / type
        Previous value: -"object"New value: +[
+  "object",
+  "null"
+]
    • Addedrelease_calendar_markets
    • Addedresolution_audit
    • Addedresolution_diff
    • Changedvariant2 fields changed
      • changedOutput schema / properties / variant / properties / transcript_consequences / items / properties / hgvsp / type
        Previous value: -"string"New value: +[
+  "string",
+  "null"
+]
      • changedOutput schema / properties / variant / properties / transcript_consequences / items / properties / is_canonical / type
        Previous value: -"boolean"New value: +[
+  "boolean",
+  "null"
+]
  4. 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."
  5. 1 tool update
    • Changedpolymarket_kalshi_spread1 field changed
      • changedInput schema / examples
        Previous value: -[
-  {
-    "topic": "fed"
-  },
-  {
-    "topic": "btc"
-  }
-]New value: +[
+  {
+    "topic": "fed"
+  },
+  {
+    "topic": "btc"
+  },
+  {
+    "topic": "bitcoin"
+  },
+  {
+    "topic": "fed rate decision"
+  }
+]
  6. 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_spread1 field changed
      • 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."

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