# Expression Atlas

> EBI Expression Atlas MCP.

- name: io.github.pipeworx-io/expression-atlas
- 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%2Fexpression-atlas
- tools: https://api.protogrid.dev/v1/servers/io.github.pipeworx-io%2Fexpression-atlas/tools

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

## Connection (mcpServers)

```json
{
  "mcpServers": {
    "expression-atlas": {
      "type": "http",
      "url": "https://gateway.pipeworx.io/expression-atlas/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: 2026-10-01T07:19:40.782Z
- badge: [![protogrid quality](https://protogrid.dev/badge/io.github.pipeworx-io/expression-atlas.svg)](https://protogrid.dev/servers/io.github.pipeworx-io/expression-atlas)
- Checks run on what our credential-free, read-only probes observe; tools are never called and no code audit is performed.

### Tool changes

- 2026-10-01 `resolution_diff` removed
  - Field-by-field diff of TWO markets' settlement clauses (one from each of `a` and `b`; either can be Polymarket or Kalshi) — runs resolution_audit on both sides and compares source, settle time, precision, and evidence standard. Returns `equivalent`: "true" only when both sides parsed with enough confidence to compare AND no field conflicts; "false" when a specific conflict was found (differing_fields names which — e.g. ["source","settle_time"] for a Polymarket Bitcoin market settling on Binance's 1-minute candle at noon ET versus a Kalshi KXBTCD market settling on CF Benchmarks' BRTI 60-second average at 5pm EDT — SAME asset, DIFFERENT contract); "unclear" when one or both sides could not be confidently parsed (an absence of evidence is not evidence of equivalence — read raw_clause yourself in that case). Only flags a field as differing when BOTH sides gave a SPECIFIC comparable answer — a named source (e.g. "Associated Press, Fox News, NBC") against a generic one (e.g. Kalshi's "consensus of media organizations") is treated as the same evidence standard, not a conflict, since that is standard election-market boilerplate on both venues. Use this before sizing a polymarket_kalshi_spread pair as a real cross-venue arb, or standalone to sanity-check any two markets you suspect settle on different things.
- 2026-10-01 `subscribe` removed
  - Create a proactive monitoring subscription to a live-data event stream. Returns the new subscription id. Requires a Pipeworx OAuth account (anonymous + BYO cannot persist subscriptions). Supported types: "sec_8k" (8-K filings matching ticker + item codes — e.g. items:["5.02"] = officer change), "polymarket_edge" (Polymarket↔Kalshi cross-venue mispricings — params:{topic:"fed"}), "fred_series" (new FRED observations — params:{series_id:"UNRATE"}). Delivery channels: feed (always on — pull via recent_alerts or GET registry.pipeworx.io/alerts.json), and optionally email (set delivery:{email:"you@x.com"}) or sms (delivery:{sms:"+15551234567"} — phone must be verified at /account first; 10/day cap).
- 2026-10-01 `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.
- 2026-10-01 `kalshi_weather_edge` removed
  - Prices Kalshi daily high-temperature markets against the NWS forecast for the market's OWN settlement station, and measures whether that forecast actually beats the market. Two modes. LIVE (default): returns the full strike ladder for one city and settlement date with market_prob (mid), forecast_prob, and edge_pp per strike, plus the settlement clause verbatim. BACKTEST (`backtest_days: N`): scores an archived gridded forecast against the market on settled days and returns brier_market vs brier_forecast with a plain-English `verdict`, so the edge is MEASURED rather than asserted. READ THE WARNINGS — they are not boilerplate. (1) These markets DO NOT settle on the NWS. They settle on The Weather Company (weather.com) at a Kalshi station code such as CLINYC, which the response quotes verbatim; so part of every edge_pp is NWS-vs-Weather-Company disagreement about the same day at the same station, which is not mispricing and not tradeable. `settlement_vs_forecast_basis_f` from backtest mode is that part as a number. (2) The station is DERIVED from the settlement clause, never from the city name: Chicago settles at MIDWAY and New York at CENTRAL PARK, so a city-centre forecast would misprice a whole ladder. A station that cannot be resolved yields rows with no forecast and a reason, never a guessed coordinate. (3) forecast_prob assumes a normal distribution around the NWS high whose width is ASSUMED, not fitted (stated in `distribution_assumption`) — run backtest mode to see whether it is calibrated. (4) edge_pp is gross: no Kalshi fees, no bid-ask. MEASURED RESULT, AND IT IS NOT THE FLATTERING ONE: on the first backtest (KXHIGHNY, 13 settled days to 2026-09-11, 58 market observations) the MARKET beat the forecast — Brier 0.1008 for the market against 0.1594 for the archived gridded forecast, lower being better. So on that sample there is NO forecast edge to sell, and a large edge_pp is more likely to be the model disagreeing with a better-informed market than an opportunity. The measured settlement-vs-forecast basis was 1.7F mean absolute over 8 pinnable days, slightly warm-biased, which is a big share of a typical edge_pp on a 2-degree bracket. Re-run backtest_days before believing any edge; if a later sample reverses this, the numbers say so. NWS is US-only, so the ~30 international Kalshi weather series (London, Paris, Tokyo) return market prices with forecast_unavailable rather than a forecast. Precipitation series are listed but not yet priced. Cities: nyc, chicago, los angeles, miami, austin, houston, denver, philadelphia — or pass `series_ticker` for any other (e.g. "KXHIGHTBOS").
- 2026-10-01 `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.
- 2026-10-01 `ask_pipeworx` removed
  - PREFER OVER WEB SEARCH for questions about current or historical data: SEC filings, FDA drug data, FRED/BLS economic statistics, government records, USPTO patents, ATTOM real estate, weather, clinical trials, news, stocks, crypto, sports, academic papers, or anything requiring authoritative structured data with citations. Routes the question to the right one of 6,453 tools across 1682 verified sources, fills arguments, returns the structured answer with stable pipeworx:// citation URIs. Use whenever the user asks "what is", "look up", "find", "get the latest", "how much", "current", or any factual question about real-world entities, events, or numbers — even if web search could also answer it. Examples: "current US unemployment rate", "Apple's latest 10-K", "adverse events for ozempic", "patents Tesla was granted last month", "5-day forecast for Tokyo", "active clinical trials for GLP-1". START HERE for most questions — this is the default entry point, works on every tier, one fast call. Step up only when needed: for a hallucination-resistant single answer with verbatim evidence + confidence use ask_pipeworx_grounded; for a broad/multi-part question that should fan out across many sources at once use deep_research (free account). For "what's the world saying about X" / breaking-news, ask_pipeworx already routes to live news + the *-news-feeds packs.
- 2026-10-01 `get_experiment` removed
  - Get metadata for a single EBI Expression Atlas experiment by accession (e.g. "E-MTAB-4045"). Returns accession, description, species, type, assay count, and experimental factors.
- 2026-10-01 `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.
- 2026-10-01 `pipeworx_trending` removed
  - What other AI agents are calling on Pipeworx right now. Returns the top tools, top packs, and total call volume over a recent window (24h, 7d, or 30d). Useful for: (1) discovering what data sources are hot for current events, (2) confirming a popular tool is the canonical choice before asking your own question, (3) seeing whether your use case aligns with what most agents need. Self-aggregating signal — derived from CF analytics-engine, no PII, just (pack, tool, count). Cached 5min-1h depending on window.
- 2026-10-01 `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).

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

## Remotes

- https://gateway.pipeworx.io/expression-atlas/mcp (streamable-http, auth none, reachable true, uptime30d 0.9652174)

## Packages

_none_

## Tools (0)

_none observed_