Search / io.github.pipeworx-io/ncbi-eutils
Ncbi Eutils
R0· no sign-inNCBI E-utilities MCP — federated Entrez search/fetch.
v0.1.3 · active · repository · website · descriptor JSON · versions
Search / io.github.pipeworx-io/ncbi-eutils
R0· no sign-inNCBI E-utilities MCP — federated Entrez search/fetch.
v0.1.3 · active · repository · website · descriptor JSON · versions
{
"mcpServers": {
"ncbi-eutils": {
"type": "http",
"url": "https://gateway.pipeworx.io/ncbi-eutils/mcp"
}
}
}claude mcp add --transport http ncbi-eutils https://gateway.pipeworx.io/ncbi-eutils/mcp[mcp_servers.ncbi-eutils]
url = "https://gateway.pipeworx.io/ncbi-eutils/mcp"
{
"$schema": "https://opencode.ai/config.json",
"mcp": {
"ncbi-eutils": {
"type": "remote",
"url": "https://gateway.pipeworx.io/ncbi-eutils/mcp",
"enabled": true
}
}
}{
"mcpServers": {
"ncbi-eutils": {
"type": "http",
"url": "https://gateway.pipeworx.io/ncbi-eutils/mcp"
}
},
"deeplink": "cursor://anysphere.cursor-deeplink/mcp/install?name=ncbi-eutils&config=eyJ0eXBlIjoiaHR0cCIsInVybCI6Imh0dHBzOi8vZ2F0ZXdheS5waXBld29yeC5pby9uY2JpLWV1dGlscy9tY3AifQ%3D%3D"
}{
"servers": {
"ncbi-eutils": {
"type": "http",
"url": "https://gateway.pipeworx.io/ncbi-eutils/mcp"
}
}
}{
"mcpServers": {
"ncbi-eutils": {
"httpUrl": "https://gateway.pipeworx.io/ncbi-eutils/mcp"
}
}
}extensions:
"ncbi-eutils":
enabled: true
name: "ncbi-eutils"
type: streamable_http
uri: "https://gateway.pipeworx.io/ncbi-eutils/mcp"
timeout: 300
Not scored: fewer than three checks apply, usually because no remote answered a credential-free probe or the server is a local package.
protocol.modernnewest supported version is 2025-03-26; 2026-07-28 not supported, older versions are deprecated until 2027-07-28protocol.statelessonly applies to 2026-07-28 serversprotocol.transportstreamable HTTPprotocol.list_ttlonly applies to 2026-07-28 serversauth.prm, auth.as_metadata, auth.cimdno remote uses OAuthauth.secret_in_urlno templated URLtools.descriptions, tools.description_length, tools.schemas, tools.annotations, tools.directory_hints, tools.token_cost, tools.api_dumptool list unknown (behind auth, not probed, or empty)stability.changes, stability.rug_pulltool list unknowndeps.known_vulns, deps.mcp_sdk_version, deps.resolvableno npm or PyPI packageresolution_auditremovedExtract 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.
geo_seriesremovedLook up an NCBI GEO (Gene Expression Omnibus) series by its GSE accession, e.g. GSE75310 -> title, organism, number of samples and their GSM ids, platform (GPL id and name), experiment type (expression profiling by array / high-throughput sequencing, methylation, ChIP-seq...), release date, summary, PubMed ids, BioProject and SRA study links. Use for any question naming a GSE expression series.
esummaryremovedFetch document summaries for one or more Entrez UIDs in a given database (e.g. pubmed), returning title, authors, journal, and publication date without the full record body.
esearchremovedSearch an Entrez database (e.g. pubmed, gene, nucleotide) by query term and return a list of matching UIDs (up to 10,000) with hit count. Supports pagination via retstart and sort (e.g. pub_date).
ai_visibility_checkremovedProbe one or more LLMs for what they know about a business / brand / product / topic and score visibility (0-100) per model. Default model is Workers AI Llama-3.3-70b (free); pass `_apiKey` to also probe Anthropic (BYO key — you pay Anthropic directly for those calls). Returns per-model {score, confidence, signals, raw_response} + a combined view. Useful for AI-marketing audits, pre-launch brand checks, competitive monitoring.
archive_compareremovedWhat changed on a web page between two dates? Resolves the archived capture nearest each date (Internet Archive Wayback Machine, Common Crawl, Arquivo.pt), extracts the readable text of both, and returns a text-level diff: the segments removed and added, a similarity score, and both capture timestamps with their gaps from the requested dates. It diffs readable text, not markup, so a restyled page with the same words reads changed:false. Identical captures answer changed:false with the reason (same capture, identical content digest, or identical text), never an empty diff. A date with no capture within max_gap_days (default 30) answers status "no_capture", naming which side is missing and the nearest captures to it. Typical uses: how a privacy policy, terms of service, pricing or product page changed; whether a statement was on a page at a given time.
archive_evidenceremovedWhat did a web page say on a given date? Finds the archived capture of a URL nearest that date across the Internet Archive Wayback Machine, Common Crawl and Arquivo.pt, reads it, and returns the readable text (HTML stripped) with the capture timestamp, a link to the archived copy, and the GAP between the date asked for and the capture actually used (e.g. "Captured 1.5 day(s) before the requested date"). One call replaces the find-capture, fetch-record, parse-HTML chain. If no archive holds a capture within max_gap_days (default 30) it answers status "no_capture" and names the nearest capture before and after the date with their gaps, so a distant capture is never passed off as the page on that date. Every archive's outcome is listed in sources[]; one that timed out or errored says so with its upstream status, and if all of them failed the answer is error "archives_unavailable", not no_capture. Captures are immutable and cached by capture id; served_from says whether the text came from cache or upstream. Use archive_compare to see what changed between two dates.
scan_dependencyremovedComposite "should I add this npm package to my project" check in ONE call — fans out across deps.dev (license + advisories + version history) and bundlephobia (gzipped/minified bundle size, dependency count, ESM/tree-shake support). Use whenever an agent asks "is X safe / popular / small" or "what does adding lodash cost me". Returns a summary block (is_latest, license, published_at, advisory_count, bundle_kb_min, bundle_kb_gz, dependency_count, has_esm, tree_shakeable), per-advisory detail, links, and a list of recent alternative versions. NPM ecosystem only in v1; PyPI / Maven / Cargo / Go fall under deps.dev:version directly. Partial failures degrade gracefully — bundlephobia's first measurement on a new version can take 5-30s; sources_failed will list it if it times out, the rest still returns.
entity_profileremoved"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 (the latest ANNUAL Revenues, NetIncomeLoss, Cash, diluted EPS, capex and operating cash flow, each with its period_end, SEC form and the accession of the filing it came from — plus EntityCommonStockSharesOutstanding, which is the newest COVER-PAGE share count the filer has published rather than an annual one, so its period_end is a cover date after the quarter closed and it is the right per-share denominator; a filer tagging a fallback concept appears under the name of that tag instead, e.g. PaymentsToAcquireProductiveAssets instead of PaymentsToAcquirePropertyPlantAndEquipment); 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.
unsubscriberemovedCancel 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.
Showing the latest 10. Full history: list_changes · trend: quality JSON.
Checks run on what our credential-free, read-only probes observe; tools are never called and no code audit is performed. How it is computed.
+repository +namespace-matches-repo +website +reachable +uptime-98% +updated-11d-ago
Derived from observable signals (official registry feed and our own credential-free probes); no code audit performed. How it is computed.
| remote | auth | reachable | uptime 30d | p50 | protocol | last ok |
|---|---|---|---|---|---|---|
https://gateway.pipeworx.io/ncbi-eutils/mcp streamable-http | none | yes | 98% | 32 ms | 2025-03-26 | 2026-10-20 |
No tools observed. Tools appear once a credential-free probe can list them.
Schemas: list_tools.
And 1,855 more from this publisher.
{
"name": "io.github.pipeworx-io/ncbi-eutils",
"title": "Ncbi Eutils",
"$schema": "https://static.modelcontextprotocol.io/schemas/2025-12-11/server.schema.json",
"remotes": [
{
"url": "https://gateway.pipeworx.io/ncbi-eutils/mcp",
"type": "streamable-http"
}
],
"version": "0.1.3",
"repository": {
"url": "https://github.com/pipeworx-io/mcp-ncbi-eutils",
"source": "github"
},
"websiteUrl": "https://pipeworx.io/packs/ncbi-eutils",
"description": "NCBI E-utilities MCP — federated Entrez search/fetch."
}