# Pubtator (npm · @pipeworx/mcp-pubtator)

PubTator 3 MCP — biomedical entity search, literature search with entity highlighting, and…

- Trust score: 79/100 (medium)
- Registry status: active
- Liveness: live
- Owner verified: no
- Last scored: 2026-11-05

## Components

- remote · `gateway.pipeworx.io`: 70/100, [markdown](https://verifymcp.io/servers/pipeworx-io-pubtator/pubtator-mcp.md), [page](https://verifymcp.io/servers/pipeworx-io-pubtator/pubtator-mcp)
- npm · `@pipeworx/mcp-pubtator`: 79/100 (this document), [markdown](https://verifymcp.io/servers/pipeworx-io-pubtator/pipeworx-mcp-pubtator.md), [page](https://verifymcp.io/servers/pipeworx-io-pubtator/pipeworx-mcp-pubtator)

## Channel facts

- Registry: `npm`
- Package: `@pipeworx/mcp-pubtator`
- Version: `0.2.1`
- Transport: `stdio`

## Trust breakdown

How this component scores in each security and reliability category. Every signal is checked automatically from public evidence about the published package, including repeated runs of it in an isolated sandbox, and we only credit what we can confirm. Scores are 0–100 per category. Scoring method: https://verifymcp.io/docs/scoring (what has changed: https://verifymcp.io/docs/scoring/changelog)

Scored 2026-11-05.

- **Supply Chain Security**: 100/100
  - No malware found by supply-chain analysis.
  - No known CVEs affecting this package version or its production dependencies.
  - No install/post-install scripts declared.
  - No production dependencies, so there is no dependency health to assess.
- **Provenance & Transparency**: 97/100
  - Source repository is publicly reachable at the declared URL.
  - Cryptographically verified build provenance (signed, bound to pipeworx-io/mcp-pubtator).
  - Clear OSI-approved license (MIT).
  - Actively maintained (last published 0 days ago).
  - Disclosure check failed: no security disclosure policy was found in the source repository.
- **Schema Quality & AI Usability**: 62/100
  - AI-judged instruction clarity (excellent).
  - Context-footprint check failed: tool/resource definitions use about 1341 tokens (~268/item across 5 items; 5 tools + 0 resources), over budget; trim descriptions and params.
  - Usage-examples check failed: none of the tools include examples.
- **Stability & Change Management**: 3/100
  - Stability observed for 1 of 30 days with no destabilising changes; credit accrues until the full window elapses.
- **Tool Coverage**: 100/100
  - 100% of tools have a non-trivial description (not blank, and not just the tool's name).
  - 100% of tool parameters carry a description.
- **Tool Safety**: 100/100
  - No prompt-injection markers were found in the server instructions, tool names or descriptions we captured.
  - We read all 5 captured tool definition(s), and no name or description among them implies an irreversible operation.
  - An AI judge read all 6 captured unit(s) of tool text and found none that tries to manipulate the model reading it.
- **Capabilities**: 100/100
  - Implements a supported MCP spec version (2025-11-25); the latest is 2026-07-28.

## Install

### How do I install the Pubtator MCP server?

Pubtator runs locally as an npm package, launched with npx -y @pipeworx/mcp-pubtator. Ready-made configuration for Claude, Cursor, VS Code, Codex and 5 more is on this page, copied from each client's own documentation.

### Claude

```bash
claude mcp add pipeworx-io-pubtator -- npx -y @pipeworx/mcp-pubtator
```

### Cursor

```json
{
  "mcpServers": {
    "pipeworx-io-pubtator": {
      "command": "npx",
      "args": [
        "-y",
        "@pipeworx/mcp-pubtator"
      ]
    }
  }
}
```

### VS Code

```json
{
  "servers": {
    "pipeworx-io-pubtator": {
      "command": "npx",
      "args": [
        "-y",
        "@pipeworx/mcp-pubtator"
      ]
    }
  }
}
```

### Codex

```bash
codex mcp add pipeworx-io-pubtator -- npx -y @pipeworx/mcp-pubtator
```

### opencode

```json
{
  "$schema": "https://opencode.ai/config.json",
  "mcp": {
    "pipeworx-io-pubtator": {
      "type": "local",
      "command": [
        "npx",
        "-y",
        "@pipeworx/mcp-pubtator"
      ],
      "enabled": true
    }
  }
}
```

### OpenClaw

```bash
openclaw mcp add pipeworx-io-pubtator --command npx --arg -y --arg @pipeworx/mcp-pubtator
```

### Hermes

```yaml
mcp_servers:
  pipeworx-io-pubtator:
    command: "npx"
    args: ["-y", "@pipeworx/mcp-pubtator"]
```

### Netclaw

```json
{
  "McpServers": {
    "pipeworx-io-pubtator": {
      "Transport": "stdio",
      "Command": "npx",
      "Arguments": [
        "-y",
        "@pipeworx/mcp-pubtator"
      ]
    }
  }
}
```

### Vellum

```bash
assistant mcp add pipeworx-io-pubtator -t stdio -c npx -a -y @pipeworx/mcp-pubtator
```

### Other

```json
{
  "mcpServers": {
    "pipeworx-io-pubtator": {
      "command": "npx",
      "args": [
        "-y",
        "@pipeworx/mcp-pubtator"
      ]
    }
  }
}
```

## Changelog

Every change recorded for this component, newest first. Days that predate change tracking, or that we cannot explain, say so: "we were watching and nothing happened" and "we were not watching" are different claims.

### 2026-11-04 (score 79)

First indexed and scored.

## MCP tools (5)

### `pubtator_find_entity` (~240 tokens)

Resolve a gene, disease, chemical/drug, variant, species or cell-line name to its normalized PubTator 3 entity id (e.g. "BRCA1" -> @GENE_BRCA1, NCBI Gene 672; "breast cancer" -> @DISEASE_Breast_Neoplasms, MeSH D001943). Use the id with pubtator_search and pubtator_relations. Sourced from the PubTator 3 autocomplete index at NCBI/NLM, which normalizes to NCBI Gene, MeSH, LitVar/dbSNP and NCBI Taxonomy. Keyless.

Input parameters:

- `concept` (string): Restrict to one entity type. Omit to search all six. gene, disease, chemical and variant are densely covered; species and cellline autocomplete is sparse.
- `limit` (number): Max matches to return, 1-25 (default 10).
- `query` (string, required): Name or synonym to look up, e.g. "BRCA1", "metformin", "breast cancer", "V600E".

### `pubtator_search` (~266 tokens)

Search PubMed/PMC literature by biomedical entity and get back, for each paper, the sentence that matched with its entity mentions decoded (gene, disease, chemical, variant, species, cell line — each normalized to an id). Query by plain text ("metformin alzheimer"), by PubTator entity ids combined with AND/OR ("@GENE_BRCA1 AND @DISEASE_Breast_Neoplasms"), or by a relation ("relations:treat|@CHEMICAL_Doxorubicin|@DISEASE_Breast_Neoplasms"). 10 results per page; total count and page count returned. Sourced from the PubTator 3 search index at NCBI/NLM (~36M PubMed abstracts + PMC open-access full text). Keyless.

Input parameters:

- `page` (number): Result page, 1-based (default 1). 10 results per page.
- `query` (string, required): Free text, or PubTator entity ids joined with AND / OR (e.g. "@GENE_BRCA1 AND @DISEASE_Breast_Neoplasms"), or a relation query "relations:<type>|<entity1>|<entity2>". Get ids from pubtator_find_entit…

### `pubtator_relations` (~352 tokens)

List the relations PubTator 3 has extracted for a gene, disease, chemical or variant — which drugs treat a disease, which genes a disease is associated with, which chemicals inhibit a gene — ranked by supporting-publication count, each labelled machine-extracted, and the top relations carrying their supporting passages (the actual sentences, with PMIDs). Filter by relation type (treat, cause, associate, interact, inhibit, stimulate, prevent, positive/negative_correlate, cotreat, drug_interact, compare) and/or by a second entity. Accepts a PubTator id (@GENE_BRCA1) or a plain name. Sourced from the PubTator 3 relation-extraction model at NCBI/NLM — predictions from text, not curated. Keyless.

Input parameters:

- `entity` (string, required): The entity to list relations for: a PubTator id ("@GENE_BRCA1", "@CHEMICAL_Doxorubicin") or a plain name ("BRCA1", "doxorubicin") — a name is resolved via autocomplete and reported in resolved_from.
- `evidence_for` (number): How many of the top relations get supporting passages attached (one search each), 0-5 (default 3). Each attaches up to 3 passages with PMIDs.
- `limit` (number): Max relations to return, 1-50 (default 20).
- `target` (string): Optional second entity to restrict to (id or plain name), e.g. "@DISEASE_Breast_Neoplasms".
- `type` (string): Restrict to one relation type. Omit for all types.

### `pubtator_relation_evidence` (~235 tokens)

The supporting passages behind one specific PubTator 3 relation — every paper whose text the model read the relation from, with the matched sentence, both entities' mentions, PMID, journal and date. Give the relation type and both entities (ids or plain names); page through the results 10 at a time. Use after pubtator_relations to audit a predicted relation. Sourced from the PubTator 3 search index at NCBI/NLM; the relation itself is machine-extracted, not curated. Keyless.

Input parameters:

- `entity1` (string, required): First entity — PubTator id or plain name, e.g. "@CHEMICAL_Doxorubicin".
- `entity2` (string, required): Second entity — PubTator id or plain name, e.g. "@DISEASE_Breast_Neoplasms". Order does not matter.
- `page` (number): Result page, 1-based (default 1). 10 passages per page.
- `type` (string, required): Relation type, e.g. "treat", "associate", "inhibit".

### `pubtator_annotations` (~193 tokens)

Entity annotations for specific PubMed articles: every gene, disease, chemical, variant, species and cell-line mention in the title and abstract (or PMC full text), each normalized to NCBI Gene / MeSH / dbSNP / Taxonomy ids with its character offsets, plus any relations PubTator 3 extracted within the article. Up to 20 PMIDs per call. Sourced from the PubTator 3 BioC JSON export at NCBI/NLM; all annotations are machine-extracted. Keyless.

Input parameters:

- `full_text` (boolean): Return PMC open-access full-text passages when available (default false: title + abstract only). Full text can be 100+ passages; each passage is truncated to 1,500 characters.
- `pmids` (array, required): PubMed ids, 1-20, e.g. ["31022191", "25616998"].

## Diagnostics

Captured diagnostic sections: Provenance, Dependencies. The full working is on the page: https://verifymcp.io/servers/pipeworx-io-pubtator/pipeworx-mcp-pubtator#diagnostics

## Score history

- 2026-11-05: 79
- 2026-11-04: 79

## Common questions

### 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 highlighting, and… This page covers its npm package (@pipeworx/mcp-pubtator).

### Is the Pubtator MCP server safe to use?

Pubtator scores 79 out of 100 on VerifyMCP. We found no known CVEs affecting it as of 5 November 2026. It declares no install or post-install scripts. Its build provenance is signed and verified. 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 5 tools: pubtator_find_entity, pubtator_search, pubtator_relations, pubtator_relation_evidence, pubtator_annotations. Their descriptions and schemas cost roughly 1,286 tokens of context every time the server is loaded.

### Is the Pubtator MCP server still maintained?

Pubtator is still listed as active in the MCP registry. We last reached this channel on 5 November 2026. Those dates come from our own scans of the registry and the channel itself, not from anything the publisher announced.

### What licence is the Pubtator MCP server under?

Pubtator declares the MIT licence, which is OSI-approved. That covers the source only, and says nothing about the cost of any service it calls.

## Links

- npm package: https://www.npmjs.com/package/@pipeworx/mcp-pubtator
- Socket report: https://socket.dev/npm/package/@pipeworx/mcp-pubtator
- Repository: https://github.com/pipeworx-io/mcp-pubtator
- Website: https://pipeworx.io/packs/pubtator
- Changelog RSS feed: https://verifymcp.io/servers/pipeworx-io-pubtator/pipeworx-mcp-pubtator.xml
- Changelog JSON feed: https://verifymcp.io/servers/pipeworx-io-pubtator/pipeworx-mcp-pubtator.json
- HTML version of this page: https://verifymcp.io/servers/pipeworx-io-pubtator/pipeworx-mcp-pubtator