Pubtator
NPM · @PIPEWORX/MCP-PUBTATOR · 2 COMPONENTS
PubTator 3 MCP — biomedical entity search, literature search with entity highlighting, and…
Available components
Last scanned (6 hours ago)
Scores higher than 61% of npm servers
Category Health and Science
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. How we score → Why this is hard to score →
Supply Chain Security100
- No malware found by supply-chain analysis.Pass
- No known CVEs affecting this package version or its production dependencies.Pass
- No install/post-install scripts declared.Pass
- No production dependencies, so there is no dependency health to assess. View diagnostics → Pass
Provenance & Transparency97
- Source repository is publicly reachable at the declared URL. View diagnostics → Pass
- Cryptographically verified build provenance (signed, bound to pipeworx-io/mcp-pubtator). View diagnostics → Pass
- Clear OSI-approved license (MIT).Pass
- Actively maintained (last published 0 days ago).Pass
- Disclosure check failed: no security disclosure policy was found in the source repository. See how to fix → Fail
Schema Quality & AI Usability62
- AI-judged instruction clarity (excellent).Pass
- 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. See how to fix → Fail
- Usage-examples check failed: none of the tools include examples. See how to fix → Fail
Stability & Change Management3
- Stability observed for 1 of 30 days with no destabilising changes; credit accrues until the full window elapses.Partial
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
Tool Safety100
- No prompt-injection markers were found in the server instructions, tool names or descriptions we captured.Pass
- We read all 5 captured tool definition(s), and no name or description among them implies an irreversible operation.Pass
- An AI judge read all 6 captured unit(s) of tool text and found none that tries to manipulate the model reading it.Pass
Capabilities100
- Implements a supported MCP spec version (2025-11-25); the latest is 2026-07-28.Pass
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.
- 4 Nov 26 79
First indexed and scored.
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 5 Nov 2026 · Analysed npm/@pipeworx/mcp-pubtator@0.2.1
Provenance Verified
A signed build attestation was found and verified, binding this exact artifact to the source repository it claims to come from.
| Result | Verified |
|---|---|
| Ecosystem | npm |
| Reason | Verified |
| Discovered via | Registry attestation endpoint |
| Source repo | pipeworx-io/mcp-pubtator |
| Certificate issuer | https://token.actions.githubusercontent.com |
| Certificate SAN | https://github.com/pipeworx-io/mcp-pubtator/.github/workflows/publish.yml@refs/heads/main |
| Rekor log index | 3691868196 |
| Predicate type | SLSA build provenance https://slsa.dev/provenance/v1 |
| Subject digest | sha512:fb9a458385d2590510a765e1aa74da2ae99484535c883a8556ababf10c03cc0f6c9d018d3e7364d2f4b4ac0fd4cd3435ac2b34d06a24880c01e3fac6a |
Background: How many MCP packages publish verified provenance →
Dependencies 0 packages
| Packages resolved | 0 |
|---|---|
| Tree resolution | Complete |
Background: SBOMs and build attestations, explained →
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 →
pubtator_annotations ~193
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.
| Name | Type | Req | Description |
|---|---|---|---|
| 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 | yes | PubMed ids, 1-20, e.g. ["31022191", "25616998"]. |
No output schema declared.
No examples provided.
pubtator_find_entity ~240
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.
| Name | Type | Req | Description |
|---|---|---|---|
| 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 | yes | Name or synonym to look up, e.g. "BRCA1", "metformin", "breast cancer", "V600E". |
No output schema declared.
No examples provided.
pubtator_relation_evidence ~235
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.
| Name | Type | Req | Description |
|---|---|---|---|
| entity1 | string | yes | First entity — PubTator id or plain name, e.g. "@CHEMICAL_Doxorubicin". |
| entity2 | string | yes | 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 | yes | Relation type, e.g. "treat", "associate", "inhibit". |
No output schema declared.
No examples provided.
pubtator_relations ~352
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.
| Name | Type | Req | Description |
|---|---|---|---|
| entity | string | yes | 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. |
No output schema declared.
No examples provided.
pubtator_search ~266
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.
| Name | Type | Req | Description |
|---|---|---|---|
| page | number | – | Result page, 1-based (default 1). 10 results per page. |
| query | string | yes | 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… |
No output schema declared.
No examples provided.
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.
npm · @pipeworx/mcp-pubtator
claude mcp add pipeworx-io-pubtator -- npx -y @pipeworx/mcp-pubtator
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.