Pubtator
REMOTE · GATEWAY.PIPEWORX.IO
PubTator 3 MCP — biomedical entity search, literature search with entity
Available components
Last scanned (14 hours ago)
Scores higher than 46% of remote servers
Reachable. Last reached 18 Oct 2026.
Category Health and Science
Recent critical change
Authorization (13 Oct 2026). See the changelog before you install this server.
How this component scores in each security and reliability category. Every signal is checked automatically against the live server, and we only credit what we can confirm. How we score → Why this is hard to score →
Endpoint Security46
- The endpoint's TLS certificate is valid, in date, and uses a strong key. View diagnostics → Pass
- Authorisation check failed: no authorisation is required to call this server, and it exposes a tool marked destructive (forget). See how to fix → View diagnostics → Fail
- HTTPS check failed: the endpoint is reachable over plaintext HTTP. See how to fix → View diagnostics → Fail
- HSTS check failed: the Strict-Transport-Security header is absent. See how to fix → View diagnostics → Fail
- DNSSEC check failed: this domain isn't protected by DNSSEC. See how to fix → View diagnostics → Fail
Transport & Reachability100
- Verified streamable-http transport via a live MCP handshake. View diagnostics → Pass
Schema Quality & AI Usability83
- 100% of prompts and resources have a non-trivial description (not blank, and not just the item's name).Pass
- AI-judged instruction clarity (excellent).Pass
- Context-footprint check failed: tool/resource definitions use about 21369 tokens (~464/item across 46 items; 46 tools + 0 resources), over budget; trim descriptions and params. See how to fix → Fail
- Tools include usage examples.Pass
Stability & Change Management22
- Stability check failed: schema churn in the 7 days we've observed: 0 tool removals, 0 breaking changes, 1 auth/transport breaks, 1 additions. See how to fix → Fail
Tool Coverage100
- 100% of tools have a non-trivial description (not blank, and not just the tool's name).Pass
- 100% of tool parameters carry a description.Pass
- Structured output schemas are declared (4% of tools); any adoption earns full credit.Pass
Tool Safety100
- No prompt-injection markers were found in the server instructions, tool names or descriptions we captured.Pass
- All 1 tool(s) whose name or description implies an irreversible operation declare an MCP destructiveHint annotation.Pass
- An AI judge read all 47 captured unit(s) of tool text and found none that tries to manipulate the model reading it.Pass
Capabilities40
- Spec-recency check failed: implements MCP spec 2025-03-26; the latest is 2026-07-28. See how to fix → Fail
Every change we have recorded for this component, newest first. Security-relevant changes are always shown. ▲ marks a change for the better, ▼ a change for the worse; unmarked changes are neutral.
- 18 Oct 26 0
- The server rewrote its instructions, which are the text every model session reads security
- Tool “ask_pipeworx” rewrote its description, which is the text the model reads security
- Tool “ask_pipeworx_beta” rewrote its description, which is the text the model reads security
- Tool “ask_pipeworx_grounded” rewrote its description, which is the text the model reads security
- Tool “deep_research” rewrote its description, which is the text the model reads security
- 17 Oct 26 +1
- The server rewrote its instructions, which are the text every model session reads security
- Tool “ask_pipeworx” rewrote its description, which is the text the model reads security
- Tool “ask_pipeworx_beta” rewrote its description, which is the text the model reads security
- Tool “ask_pipeworx_grounded” rewrote its description, which is the text the model reads security
- Tool “company_facts” rewrote its description, which is the text the model reads security
- Tool “deep_research” rewrote its description, which is the text the model reads security
- Tool “entity_profile” rewrote its description, which is the text the model reads security
- “company_facts” reworded the description of “attribute” cosmetic
- 16 Oct 26 0
- The server rewrote its instructions, which are the text every model session reads security
- Tool “ask_pipeworx” rewrote its description, which is the text the model reads security
- Tool “ask_pipeworx_beta” rewrote its description, which is the text the model reads security
- Tool “ask_pipeworx_grounded” rewrote its description, which is the text the model reads security
- Tool “deep_research” rewrote its description, which is the text the model reads security
- Tool “subscribe” rewrote its description, which is the text the model reads security
- “subscribe” reworded the description of “params” cosmetic
- 15 Oct 26 +1
- The server rewrote its instructions, which are the text every model session reads security
- Tool “ask_pipeworx” rewrote its description, which is the text the model reads security
- Tool “ask_pipeworx_beta” rewrote its description, which is the text the model reads security
- Tool “ask_pipeworx_grounded” rewrote its description, which is the text the model reads security
- Tool “deep_research” rewrote its description, which is the text the model reads security
- Tool “resolve_entity” now declares an output schema ▲ functional
- New tool “company_register_search” functional
- “ask_pipeworx_grounded” added an optional parameter “prefer_tool” cosmetic
- “entity_profile” added an optional parameter “country” cosmetic
- “resolve_entity” added an optional parameter “country” cosmetic
- “entity_profile” reworded the description of “value” cosmetic
- 14 Oct 26 0
- The server rewrote its instructions, which are the text every model session reads security
- Tool “ask_pipeworx” rewrote its description, which is the text the model reads security
- Tool “ask_pipeworx_beta” rewrote its description, which is the text the model reads security
- Tool “ask_pipeworx_grounded” rewrote its description, which is the text the model reads security
- Tool “deep_research” rewrote its description, which is the text the model reads security
- 13 Oct 26 +30
- Authorization: unverified → fail ▼ critical
- Stability: unverified → fail ▼ security
- Injection markers: unverified → pass ▲ security
- The server rewrote its instructions, which are the text every model session reads security
- Tool “ask_pipeworx” rewrote its description, which is the text the model reads security
- Tool “ask_pipeworx_beta” rewrote its description, which is the text the model reads security
- Tool “ask_pipeworx_grounded” rewrote its description, which is the text the model reads security
- Tool “company_facts” rewrote its description, which is the text the model reads security
- Tool “deep_research” rewrote its description, which is the text the model reads security
- Tool coverage: unverified → 100 ▲ functional
- Schema quality: unverified → 100 ▲ functional
- “ask_pipeworx” added an optional parameter “packs” cosmetic
- “ask_pipeworx_beta” added an optional parameter “packs” cosmetic
- 12 Oct 26 −43
- Authorization: pass → unverified ▼ security
- Tool safety: pass → unverified ▼ security
- Schema quality: 100 → unverified ▼ functional
- Tool coverage: 100 → unverified ▼ functional
- This server's schema is too large to store in full, so we cannot compare its tools day to day functional
- 11 Oct 26 +43
- Authorization: unverified → pass ▲ security
- Injection markers: unverified → pass ▲ security
- First check of Authorization: pass security
- First check of Judged manipulation: pass security
- Tool coverage: unverified → 100 ▲ functional
- Schema quality: unverified → 100 ▲ functional
- First check of Schema quality: excellent functional
- First check of Schema quality: fail functional
- First check of Schema quality: pass functional
- First check of Destructive annotations: 100 functional
- First check of Tool coverage: 2 functional
- First check of Tool coverage: 100 functional
- This server's schema is too large to store in full, so we cannot compare its tools day to day functional
Diagnostic detail from the automated scan of this channel: what the scanner observed at each step, so you can see exactly where a check passed or failed. It is informational only and never changes the trust score.
Captured 18 Oct 2026 · Probed https://gateway.pipeworx.io/pubtator/mcp
TLS valid
Negotiated TLS 1.3 with TLS_AES_128_GCM_SHA256 .
| Subject | Issuer | Valid from | Valid until | Key | Signature | Serial |
|---|---|---|---|---|---|---|
| CN=pipeworx.io | CN=WE1,O=Google Trust Services,C=US | 19 Sept 2026 | 18 Dec 2026 | ECDSA 256 | ECDSA-SHA256 | 907077ac952af983139424aa9b807ef7 |
| SANs: pipeworx.io, gateway.pipeworx.io, *.gateway.pipeworx.io | ||||||
| CN=WE1,O=Google Trust Services,C=US (CA) | CN=GTS Root R4,O=Google Trust Services LLC,C=US | 13 Dec 2023 | 20 Feb 2029 | ECDSA 256 | ECDSA-SHA384 | 7ff31977972c224a76155d13b6d685e3 |
| CN=GTS Root R4,O=Google Trust Services LLC,C=US (CA) | CN=GlobalSign Root CA,OU=Root CA,O=GlobalSign nv-sa,C=BE | 15 Nov 2023 | 28 Jan 2028 | ECDSA 384 | SHA256-RSA | 7fe530bf331343bedd821610493d8a1b |
Background: What to check on a remote MCP endpoint →
DNSSEC insecure
Validation of gateway.pipeworx.io. — Not signed
| Zone | DS | Keys | Algorithms | Outcome |
|---|---|---|---|---|
| . | trust_anchor | 20326, 38696 | 8, 8 | Verified |
| io. | present | 57355 | 8 | Verified |
| pipeworx.io. | absent | Unsigned (proven) parent-signed NSEC/NSEC3 proves an unsigned delegation |
Authentication No authorisation required
The endpoint answered without asking for a token. Anyone who knows the URL can reach it.
| Result | No authorisation required |
|---|---|
| HTTP status | 200 |
Background: How OAuth 2.1 works in the 2026 MCP spec →
Transports 2 probes
| Transport | URL | Outcome | Status | Location |
|---|---|---|---|---|
| streamable-http | https://gateway.pipeworx.io/pubtator/mcp | Verified | 200 | |
| http (plaintext) | http://gateway.pipeworx.io/pubtator/mcp | Served over HTTP | 200 |
The tools this component advertises to a client, with an estimated token cost for each. Expand a tool to see its parameters and schema. The per-tool counts are indicative and are not scored directly; the schema's total context footprint is one signal in Schema Quality & AI Usability. A tool's description is untrusted text the model reads on every call, which is what makes this list a security surface and not just an inventory: how tool poisoning works →
suggest_questions What Can I Ask Pipeworx? ~240
What can I ask Pipeworx? / what is Pipeworx good for? / what can you do? / give me ideas / show me examples / getting started / what data do you have? — the onboarding entry point for an agent that just connected and wants to know what is worth asking. Returns category-bucketed example questions (company financials, drugs & clinical trials, economics, real estate, prediction markets, weather, government & patents, science & academia, news) — each with the exact tool + argument shape that answers it, drawn from the live catalog of thousands of tools. Call with no arguments for the full spread, or pass `topic` (e.g. "finance", "pharma", "betting") to focus. Use this FIRST when you do not yet know what Pipeworx can do for you, or to learn how to call the meta-tools (ask_pipeworx, entity_profile, compare_entities, etc.).
| Name | Type | Req | Description |
|---|---|---|---|
| topic | string | – | Optional focus area: finance | pharma | economics | real-estate | betting | weather | government | science | news. Omit for a cross-category spread. |
No output schema declared.
{"topic":"finance"}unsubscribe Unsubscribe from Alerts ~60
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.
| Name | Type | Req | Description |
|---|---|---|---|
| id | string | yes | Subscription id (uuid) returned by subscribe. |
No output schema declared.
No examples provided.
validate_claim Validate Claim ~370
"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).
| Name | Type | Req | Description |
|---|---|---|---|
| claim | string | yes | Natural-language factual claim, e.g., "Apple's FY2024 revenue was $400 billion" or "Microsoft made about $100B in profit last year". |
| tolerance_pct | number | – | Max percent deviation still graded approximately_correct (0.5–50). Overrides the tolerance implied by the claim wording — set 1–2 for hallucination detection where any material error must be refuted.… |
No output schema declared.
{"claim":"Apple's fiscal 2023 revenue was $383 billion"}How do I install the Pubtator MCP server?
Pubtator is a hosted endpoint at https://gateway.pipeworx.io/pubtator/mcp, so there is nothing to install locally. Ready-made configuration for Claude, Cursor, VS Code, Codex and 5 more is on this page, copied from each client's own documentation.
remote · gateway.pipeworx.io
claude mcp add --transport http pipeworx-io-pubtator 'https://gateway.pipeworx.io/pubtator/mcp'
What is the Pubtator MCP server?
Pubtator is an MCP server listed in the public MCP registry as io.github.pipeworx-io/pubtator. PubTator 3 MCP, biomedical entity search, literature search with entity. This page covers its hosted endpoint (https://gateway.pipeworx.io/pubtator/mcp).
Is the Pubtator MCP server safe to use?
Pubtator scores 62 out of 100 on VerifyMCP. That is a record of what we were able to check automatically, not an endorsement. The category breakdown on this page shows every signal behind the number, including the ones we could not confirm.
What tools does the Pubtator MCP server expose?
Pubtator exposes 46 tools: ask_pipeworx, ask_pipeworx_beta, ask_pipeworx_grounded, search_within, deep_research, and 41 more. Their descriptions and schemas cost roughly 21,194 tokens of context every time the server is loaded.
Does the Pubtator MCP server require authentication?
No. We connected to Pubtator without credentials and it answered, so anything it exposes is reachable by anyone who knows the address.
Is the Pubtator MCP server still maintained?
Pubtator is still listed as active in the MCP registry. We last reached this channel on 18 October 2026. Those dates come from our own scans of the registry and the channel itself, not from anything the publisher announced.