# Biosamples

> EBI BioSamples MCP.

- name: io.github.pipeworx-io/biosamples
- version: 0.1.2
- connection class: R0 (autonomous)
- trust: 95/100
- quality: –/100 (not scored)
- owner: not claimed
- descriptor: https://api.protogrid.dev/v1/servers/io.github.pipeworx-io%2Fbiosamples
- tools: https://api.protogrid.dev/v1/servers/io.github.pipeworx-io%2Fbiosamples/tools

**An agent can connect right now, no human step.** Remote endpoint, no authentication, reachable on the last probe.

## Connection (mcpServers)

```json
{
  "mcpServers": {
    "biosamples": {
      "type": "http",
      "url": "https://gateway.pipeworx.io/biosamples/mcp"
    }
  }
}
```


## Trust

- hygiene: 100
- liveness: 99
- freshness: 100
- provenance: 85
- drivers: +repository +namespace-matches-repo +website -thin-description +reachable +uptime-97% +updated-24d-ago
- Derived from observable signals (official registry feed and our own credential-free probes); no code audit performed.

## Quality –/100 (not scored)

Not scored: fewer than three checks apply, usually because no remote answered a credential-free probe or the server is a local package.

### protocol: 75 (weight 25)

- warn `protocol.modern`: newest supported version is 2025-03-26; 2026-07-28 not supported, older versions are deprecated until 2027-07-28
- n/a `protocol.stateless`: only applies to 2026-07-28 servers
- pass `protocol.transport`: streamable HTTP
- n/a `protocol.list_ttl`: only applies to 2026-07-28 servers

### authorization: n/a (weight 15)

- n/a `auth.prm`, `auth.as_metadata`, `auth.cimd`: no remote uses OAuth
- n/a `auth.secret_in_url`: no templated URL

### tool hygiene: n/a (weight 30)

- n/a `tools.descriptions`, `tools.description_length`, `tools.schemas`, `tools.annotations`, `tools.directory_hints`, `tools.token_cost`, `tools.api_dump`: tool list unknown (behind auth, not probed, or empty)

### stability: n/a (weight 15)

- n/a `stability.changes`, `stability.rug_pull`: tool list unknown

### dependencies: n/a (weight 15)

- n/a `deps.known_vulns`, `deps.mcp_sdk_version`, `deps.resolvable`: no npm or PyPI package

- tools: unknown
- tools last changed: 2026-09-29T07:26:44.939Z
- badge: [![protogrid quality](https://protogrid.dev/badge/io.github.pipeworx-io/biosamples.svg)](https://protogrid.dev/servers/io.github.pipeworx-io/biosamples)
- Checks run on what our credential-free, read-only probes observe; tools are never called and no code audit is performed.

### Tool changes

- 2026-09-29 `get_sample` removed
  - Fetch a single EBI BioSamples record by accession. Returns the sample name, dates, taxId, organism, and a flattened map of its characteristics (organism, tissue, sex, cell type, etc.). Keyless.
- 2026-09-29 `validate_claim` removed
  - "Is it true that…" / "fact check" / "verify the claim that…" / "did X really…" / "was Y actually…" / "confirm or refute" / "true or false" — natural-language claim verification against authoritative sources. Use whenever the agent needs to check whether something a user said is factually correct. Company-financial claims (revenue, net income, cash for public US companies) verify via the structured SEC EDGAR + XBRL fast path with exact percent-delta math; ANY OTHER factual claim (macro statistics, rates, prices, drug data, records) automatically falls through to the grounded pipeline — routed to the right live source, answered with verbatim evidence, then judged. Returns a verdict (confirmed / approximately_correct / refuted / inconclusive / unsupported / could_not_verify), the grounded or structured actual value with pipeworx:// citation, and reasoning. IMPORTANT for callers: could_not_verify means the check did not happen (our LLM or source failed) and carries verification_error{stage,detail} — it is NOT evidence for or against the claim, and must not be shown as one. unsupported means we looked and cover no source for it. Replaces 4–6 sequential calls (NL parsing → entity resolution → data lookup → comparison).
- 2026-09-29 `forget` removed
  - Delete a previously stored memory by key. Use when context is stale, the task is done, or you want to clear sensitive data the agent saved earlier. Pair with remember and recall.
- 2026-09-29 `pipeworx_feedback` removed
  - Tell the Pipeworx team something is broken, missing, or needs to exist. Use when a tool returns wrong/stale data (bug), when a tool you wish existed isn't in the catalog (feature/data_gap), or when something worked surprisingly well (praise). ONLY for tools served by this Pipeworx connection — if the tool came from a different MCP server in your client (another vendor's Gmail, Splunk, Slack, etc. connector), we cannot fix it and reporting it here only delays you; file it with that server instead. Not sure? Pipeworx tool names are the ones this connection lists. Describe the issue in terms of Pipeworx tools/packs — don't paste the end-user's prompt. Filing without an account returns a `claim_token`; pass it back later as pipeworx_feedback({claim_token:"pwfb_…"}) to read whether it was fixed and what changed. The team reads digests daily and signal directly affects roadmap. Rate-limited to 5 per identifier per day. Free; doesn't count against your tool-call quota.
- 2026-09-29 `scan_competitor_ai_presence` removed
  - Compare AI visibility across multiple entities side-by-side. Probes each entity (your brand + N competitors) with ai_visibility_check, ranks by score, surfaces which is most/least recognized. Useful for competitive AI-marketing audits: "does Claude know about us as well as our competitors?". Returns ranked list with score, confidence, signal density per entity.
- 2026-09-29 `resolution_audit` removed
  - Extract the settlement clause of a single Polymarket or Kalshi market: who publishes the settling number (source), the clock time + timezone it is taken at, the precision of the computation (e.g. "1-minute candle close" vs "60-second trailing average" vs "election outcome"), the evidence standard (official_source | consensus_reporting | any_credible_report | unspecified), and void_handling (cancellation/postponement settlement — reused verbatim from bet_research's cancellation_rule detector, not re-derived). Parses Polymarket's `description` field (fetched via polymarket_market) or Kalshi's `rules_primary` + `rules_secondary` fields (fetched via kalshi_market) with regex + a small vocabulary — no LLM pass, so an unusual clause reports confidence:"low" rather than a guess. Pass `market` as a Polymarket slug/URL or a Kalshi market ticker (e.g. "KXBTCD-26SEP1317-T66999.99"); a Kalshi EVENT ticker (e.g. "KXBTCD-26SEP1317") also works — it picks one representative market under that event, since the settlement mechanism is normally shared across all strikes/legs in one event. Use this before treating a polymarket_kalshi_spread row as a real arbitrage: two ladders that look alike can settle on different sources, at different times, with different precision — this tool is how you check. Pair with resolution_diff to compare two markets directly. KNOWN GAP: idiosyncratic phrasing that doesn't match the vocabulary returns confidence:"low" and evidence_standard:"unspecified" rather than an LLM-guessed answer.
- 2026-09-29 `company_facts` removed
  - TYPED, DETERMINISTIC financial facts for a US public company for an EXPLICITLY NAMED reporting period — "Apple revenue for fiscal 2023", "Walmart net income FY2026 Q3", "Microsoft cash at the end of fiscal 2024". PREFER OVER entity_profile / get_company_financials whenever the period matters: those answer "the most recent figures" and will happily hand back FY2025 when you asked about FY2019, and neither separates a discrete quarter from a year-to-date figure. This one refuses instead — it NEVER substitutes the latest period for the period requested, NEVER returns 0 for missing data, NEVER lets a 9-month YTD number answer a quarterly question, and NEVER converts a currency. Every answer carries the exact us-gaap concept it came from, what that concept MEASURES (NetIncomeLoss excludes non-controlling interests, ProfitLoss includes them — not synonyms), the accession number and a link to the filing on sec.gov, the restatement trail of any superseded figures, and a contract + derivation version to pin against. Fiscal periods are the FILER'S OWN, anchored on their fiscal-year end, so Walmart's year ending 2026-01-31 is FY2026 and Apple's ending 2025-09-27 is FY2025. Attributes in v1: revenue, net_income, cash. Every non-answer is a named status — `unavailable` (the filer did not report it for that period; the periods that DO exist are listed, without values), `unsupported` (outside what v1 covers — a non-us-gaap filer, an unknown attribute, a non-USD unit), `ambiguous` (the company name matched two filers equally well; both are named), `conflicting` (two filings the same day disagree; both are returned and neither is picked), `partial` (a value with no accession behind it). Source: SEC EDGAR XBRL companyconcept, one publisher read once — see `corroboration`. Same response is served at POST https://gateway.pipeworx.io/v1/facts for non-MCP callers.
- 2026-09-29 `entity_profile` removed
  - "Tell me about X" / "research Acme" / "brief me on Tesla" / "what does Apple do" / "company profile for Microsoft" / "give me the rundown on NVDA" / "everything you know about $TICKER" — full cross-source profile of a US public company in ONE parallel call. ALWAYS PREFER over chaining single-pack SEC/XBRL/news lookups when the user asks for a holistic view. Fans out across SEC EDGAR, XBRL, USPTO patents, federal contracts (USAspending), FDA-licensed biologics (Purple Book), H-1B hiring (DOL LCA), news and GLEIF, and returns: cik + company_name (+ resolved_from/resolved_to when `value` was a name); recent_filings (up to 5 with pipeworx://edgar/company/{cik}/filings/{accession} URIs); fundamentals (LATEST 10-K Revenues + NetIncomeLoss + Cash, sorted period_end DESC); patents (USPTO PatentsView API sunset May 2025 — soft-fails until reactivated); federal_contracts (USAspending awards where the company is the recipient); fda_products (FDA-licensed biologics — vaccines, cell/gene therapies — from the Purple Book; a company with only small-molecule/generic drugs will show none here, that is expected, not a failure); hiring (H-1B sponsorship volume + salary range from DOL LCA filings); recent news mentions via GDELT→GNews fallback; LEI via GLEIF. `sources_used` / `sources_failed` say which of these actually returned data for THIS company — an empty section is a real "no data", not a bug. `sources_skipped` is the third state: a leg we deliberately did NOT run, each entry carrying a `reason` token and a plain-English `detail` (the Purple Book is skipped for a filer SEC classifies outside the life-science SIC bands, since it lists only 351(a)/(k) biologics licence holders). Pass a ticker ("AAPL"), zero-padded CIK ("0000320193"), OR a company name ("Moderna") — names now resolve via SEC EDGAR's company-name match; a private company (no CIK/ticker) returns resolved:false with an explicit `notes` line, not a bare failure. `type` accepts "company" or "ticker" interchangeably — both take the same `value` shapes above.
- 2026-09-29 `unsubscribe` removed
  - Cancel a subscription by id. Ownership is enforced — you can only cancel your own subscriptions. The row is deactivated (not deleted) so its historical events stay available via recent_alerts.
- 2026-09-29 `search_within` removed
  - Semantic search INSIDE a fetched record. Pass the text you already pulled (e.g. a SEC 10-K body, an article, a long tool result) plus a natural-language query; get back the top-N passages with character offsets and similarity scores. Use when the record is too big to cram into the prompt — search_within saves context, returns only the passages that matter, and every passage carries an offset so the agent can verify a verbatim quote. Pairs with ask_pipeworx_grounded: fetch with the gateway, ground over the relevant passages instead of the whole document. BGE-base-en embeddings + cosine over 500-char overlapping windows; cap is 200K chars (longer inputs are truncated and flagged).

Full history: https://api.protogrid.dev/v1/servers/io.github.pipeworx-io%2Fbiosamples/changes

## Remotes

- https://gateway.pipeworx.io/biosamples/mcp (streamable-http, auth none, reachable true, uptime30d 0.9741379)

## Packages

_none_

## Tools (0)

_none observed_