# Bioportal (npm · @pipeworx/mcp-bioportal)

BioPortal — NCBO's biomedical ontology repository (data.bioontology.org).

- Trust score: 83/100 (high trust)
- Change this week: +4
- Registry status: active
- Liveness: live
- Owner verified: no
- Last scored: 2026-11-05

## Components

- remote · `gateway.pipeworx.io`: 71/100, [markdown](https://verifymcp.io/servers/pipeworx-io-bioportal/bioportal-mcp.md), [page](https://verifymcp.io/servers/pipeworx-io-bioportal/bioportal-mcp)
- npm · `@pipeworx/mcp-bioportal`: 83/100 (this document), [markdown](https://verifymcp.io/servers/pipeworx-io-bioportal/pipeworx-mcp-bioportal.md), [page](https://verifymcp.io/servers/pipeworx-io-bioportal/pipeworx-mcp-bioportal)

## Channel facts

- Registry: `npm`
- Package: `@pipeworx/mcp-bioportal`
- 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-bioportal).
  - Clear OSI-approved license (MIT).
  - Actively maintained (last published 5 days ago).
  - Disclosure check failed: no security disclosure policy was found in the source repository.
- **Schema Quality & AI Usability**: 67/100
  - AI-judged instruction clarity (excellent).
  - Context-footprint check failed: tool/resource definitions use about 916 tokens (~229/item across 4 items; 4 tools + 0 resources), over budget; trim descriptions and params.
  - Usage-examples check failed: none of the tools include examples.
- **Stability & Change Management**: 23/100
  - Stability observed for 7 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 4 captured tool definition(s), and no name or description among them implies an irreversible operation.
  - An AI judge read all 5 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 Bioportal MCP server?

Bioportal runs locally as an npm package, launched with npx -y @pipeworx/mcp-bioportal. 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-bioportal -- npx -y @pipeworx/mcp-bioportal
```

### Cursor

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

### VS Code

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

### Codex

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

### opencode

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

### OpenClaw

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

### Hermes

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

### Netclaw

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

### Vellum

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

### Other

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

## 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.

### 2026-11-05 (score 83, +1)

No change was recorded against any check on this day. Stability & Change Management went from 20 to 23. That category is still filling its 30-day observation window: 6 days of observed history at the previous scan, 7 at this one. The score rises as the window fills, whether or not the server changes.

### 2026-11-03 (score 82, +1)

No change was recorded against any check on this day. Stability & Change Management went from 13 to 17. That category is still filling its 30-day observation window: 4 days of observed history at the previous scan, 5 at this one. The score rises as the window fills, whether or not the server changes.

### 2026-11-01 (score 81, +1)

No change was recorded against any check on this day. Stability & Change Management went from 7 to 10. That category is still filling its 30-day observation window: 2 days of observed history at the previous scan, 3 at this one. The score rises as the window fills, whether or not the server changes.

### 2026-10-31 (score 80, +15)

- [security improvement] Malware scan: unverified → pass

### 2026-10-30 (score 65, −14)

- [security regression] Malware scan: pass → unverified
- [functional] Package version: 0.2.0 → 0.2.1

### 2026-10-29 (score 79)

First indexed and scored.

## MCP tools (4)

### `bioportal_search` (~269 tokens)

Search ~1,300 biomedical ontologies for a term and get back the matching classes with their preferred label, synonyms, definition, ontology and permanent class IRI. AUTHORITATIVE for mapping free text to a coded clinical concept (NCIT, SNOMEDCT, LOINC, RXNORM, MESH, HPO, ICD10CM) — these are the curated terminologies themselves, not a description of them. Restrict with `ontologies` when you know which vocabulary you want.

Input parameters:

- `_apiKey` (string): Your own BioPortal API key (free, https://bioportal.bioontology.org/accounts/new). Optional — without one the call uses a shared key that NCBO rate-limits across all of its users.
- `exact_match` (boolean): Only exact label/synonym matches (default false)
- `limit` (number): Max classes to return, 1-100 (default 25)
- `ontologies` (string): Comma-separated ontology acronyms to restrict to (e.g. "NCIT,DOID,SNOMEDCT")
- `query` (string, required): Term to search for (e.g. "melanoma", "metformin")
- `require_definitions` (boolean): Only return classes that carry a definition

### `bioportal_ontologies` (~165 tokens)

List the biomedical ontologies BioPortal carries — acronym, full name and type — so you can pick the right vocabulary acronym before searching or looking up a class. AUTHORITATIVE catalogue of what is available in BioPortal. Pass `filter` to narrow by acronym or name substring.

Input parameters:

- `_apiKey` (string): Your own BioPortal API key (free, https://bioportal.bioontology.org/accounts/new). Optional — without one the call uses a shared key that NCBO rate-limits across all of its users.
- `filter` (string): Case-insensitive substring of the acronym or name (e.g. "snomed", "cancer")
- `limit` (number): Max ontologies to return, 1-200 (default 50)

### `bioportal_class` (~186 tokens)

Full record for one ontology class by its IRI — preferred label, every synonym, the curated definition, semantic types, obsolescence flag, and links to parents and children. AUTHORITATIVE for the canonical meaning of a coded concept. Pass the ontology acronym and the class IRI exactly as bioportal_search returned it.

Input parameters:

- `_apiKey` (string): Your own BioPortal API key (free, https://bioportal.bioontology.org/accounts/new). Optional — without one the call uses a shared key that NCBO rate-limits across all of its users.
- `class_id` (string, required): Full class IRI as returned by bioportal_search, e.g. "http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C3224"
- `ontology` (string, required): Ontology acronym (e.g. "NCIT")

### `bioportal_mappings` (~243 tokens)

Cross-ontology mappings for one class — the equivalent concepts in every other BioPortal ontology, with the mapping source (SAME_URI, LOOM, CUI, REST). AUTHORITATIVE for translating a code between terminologies, e.g. an NCIT concept to its SNOMEDCT, MESH and ICD10CM equivalents. Pass the ontology acronym and class IRI.

Input parameters:

- `_apiKey` (string): Your own BioPortal API key (free, https://bioportal.bioontology.org/accounts/new). Optional — without one the call uses a shared key that NCBO rate-limits across all of its users.
- `class_id` (string, required): Full class IRI (e.g. "http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C3224")
- `limit` (number): Max mappings to return, 1-200 (default 50)
- `ontology` (string, required): Ontology acronym the class lives in (e.g. "NCIT")
- `to_ontology` (string): Optional: only mappings into this ontology acronym (e.g. "SNOMEDCT")

## Diagnostics

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

## Score history

- 2026-11-05: 83
- 2026-11-04: 82
- 2026-11-03: 82
- 2026-11-02: 81
- 2026-11-01: 81
- 2026-10-31: 80
- 2026-10-30: 65
- 2026-10-29: 79

## Common questions

### What is the Bioportal MCP server?

Bioportal is an MCP server listed in the public MCP registry as io.github.pipeworx-io/bioportal. BioPortal, NCBO's biomedical ontology repository (data.bioontology.org). This page covers its npm package (@pipeworx/mcp-bioportal).

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

Bioportal scores 83 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 Bioportal MCP server expose?

Bioportal exposes 4 tools: bioportal_search, bioportal_ontologies, bioportal_class, bioportal_mappings. Their descriptions and schemas cost roughly 863 tokens of context every time the server is loaded.

### Is the Bioportal MCP server still maintained?

Bioportal 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 Bioportal MCP server under?

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

### What did VerifyMCP test on the Bioportal MCP server?

VerifyMCP ran 16 checks on Bioportal, covering Malware scan, Known CVEs, Install scripts, Dependency health and 12 more. Endpoint Security and Transport & Reachability do not apply to an npm package, so they were not tested. The score does not measure everything, and the scoring documentation lists what it leaves out.

## Links

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