Skip to main content
Glama

Biosamples

by io.github.pipeworx-io
OverviewDiscussionsAdmin

Server Details

EBI BioSamples MCP.

Glama couldn't complete the latest health check. If this server requires authentication, missing or expired test credentials may be the cause. A test profile lets Glama authenticate for health checks and discover tools; it is separate from your personal connections.

If you are the author, claim ownership, then add or update a test profile under Admin → Test Profile.

Status
Unhealthy
Uptime
30.9% over 57 days
Last Tested
Transport
Streamable HTTP
URL
Repository
pipeworx-io/mcp-biosamples
GitHub Stars
0
Server Listing
EBI BioSamples MCP

TDQS

B3.4/5.0

Scored across 38 tools

Disambiguation1/5

Only two tools (search_samples, get_sample) relate to the server's stated Biosamples purpose, and they are straightforwardly distinct. The other 36 tools heavily overlap in purpose: ask_pipeworx, ask_pipeworx_beta, ask_pipeworx_grounded, and deep_research all route factual questions, while the polymarket_* and resolution_* families repeatedly cover edge detection, arbitrage, and market settlement analysis.

Naming Consistency2/5

Some clusters follow consistent patterns (ask_pipeworx*, polymarket_*, resolution_*), but the overall set mixes verb phrases (search_samples, validate_claim, recall) with noun phrases (entity_profile, company_facts, bet_research) and includes standalone brand-style names (ask_pipeworx, generate_llms_txt). The naming is readable but has no unified convention.

Tool Count1/5

38 tools is already heavy, but the mismatch is extreme when only 2 of them actually serve the Biosamples domain. The remaining 36 tools cover prediction markets, AI visibility, npm dependencies, and general Pipeworx data retrieval, which has no obvious relationship to biological samples.

Completeness1/5

For a Biosamples server, the surface is severely incomplete: search and single-record fetch exist, but there is no submission/update, project/group access, checklist handling, or batch retrieval. The 36 unrelated tools do not fill these gaps and instead make the domain coverage appear arbitrary and incomplete.

Tool Schema Changelog

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

  1. 7 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"
+}
    • 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. 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"
+  }
+]
  3. 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."
  4. 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"
+  }
+]
  5. 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."

Related MCP Connectors

Related MCP Servers

Try in Browser
One endpoint for every MCP toolRayrun runs every MCP server behind one URL and holds the credentials. Each call is decided per client, tool, and argument, then recorded.ray.runAd

Glama MCP Gateway

Add one secure layer between your agents and this server.

Resources