# Pombase (npm · @pipeworx/mcp-pombase)

PomBase MCP — the fission yeast (Schizosaccharomyces pombe) model-organism database.

- Trust score: 84/100 (high trust)
- Change this week: +3
- Registry status: active
- Liveness: live
- Owner verified: no
- Last scored: 2026-11-05

## Components

- remote · `gateway.pipeworx.io`: 77/100, [markdown](https://verifymcp.io/servers/pipeworx-io-pombase/pombase-mcp.md), [page](https://verifymcp.io/servers/pipeworx-io-pombase/pombase-mcp)
- npm · `@pipeworx/mcp-pombase`: 84/100 (this document), [markdown](https://verifymcp.io/servers/pipeworx-io-pombase/pipeworx-mcp-pombase.md), [page](https://verifymcp.io/servers/pipeworx-io-pombase/pipeworx-mcp-pombase)

## Channel facts

- Registry: `npm`
- Package: `@pipeworx/mcp-pombase`
- 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-pombase).
  - 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**: 75/100
  - AI-judged instruction clarity (good).
  - Context-footprint check failed: tool/resource definitions use about 306 tokens (~153/item across 2 items; 2 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 2 captured tool definition(s), and no name or description among them implies an irreversible operation.
  - An AI judge read all 3 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 Pombase MCP server?

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

### Cursor

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

### VS Code

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

### Codex

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

### opencode

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

### OpenClaw

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

### Hermes

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

### Netclaw

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

### Vellum

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

### Other

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

## 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 84, +3)

- [security regression] Tool safety: pass → unverified
- [security] Stability: Stability not yet verified: we do not have a sandbox capture of the MCP schema this version of the package serves yet.
- [functional regression] Capabilities: pass → unverified
- [functional regression] Tool coverage: 100 → unverified
- [functional improvement] Stability: unverified → 0.20
- [functional] First check of Schema quality: unverified
- [functional] Package version: 0.2.0 → 0.2.1

### 2026-11-03 (score 81, 0)

- [functional regression] Security disclosure: unverified → fail

### 2026-11-01 (score 81, 0)

- [functional regression] Security disclosure: fail → unverified

### 2026-10-30 (score 81, 0)

- [functional regression] Security disclosure: unverified → fail

### 2026-10-29 (score 81)

First indexed and scored.

## MCP tools (2)

### `get_gene` (~152 tokens)

PomBase (fission yeast / S. pombe model-organism DB): look up a gene by its PomBase systematic id and return its product, protein domains (InterPro), deletion viability, UniProt id, and curation status. Keyless. NOTE: requires a systematic id like "SPAC1002.01" or "SPBC2F12.13" — standard gene names like "cdc2" are NOT resolved by this API. Complements SGD (budding yeast).

Input parameters:

- `id` (string, required): A PomBase systematic id, e.g. "SPAC1002.01" or "SPBC2F12.13". Standard names ("cdc2") are not accepted.

### `get_reference` (~100 tokens)

PomBase: look up a curated S. pombe publication by its PubMed id (e.g. "PMID:11739790") and return its title, citation, authors, year, abstract, and how many genes it annotates. Keyless.

Input parameters:

- `pmid` (string, required): A PubMed id, with or without the "PMID:" prefix, e.g. "PMID:11739790" or "11739790".

## Diagnostics

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

## Score history

- 2026-11-05: 84
- 2026-11-04: 84
- 2026-11-03: 81
- 2026-11-02: 81
- 2026-11-01: 81
- 2026-10-31: 81
- 2026-10-30: 81
- 2026-10-29: 81

## Common questions

### What is the Pombase MCP server?

Pombase is an MCP server listed in the public MCP registry as io.github.pipeworx-io/pombase. PomBase MCP, the fission yeast (Schizosaccharomyces pombe) model-organism database. This page covers its npm package (@pipeworx/mcp-pombase).

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

Pombase scores 84 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 Pombase MCP server expose?

Pombase exposes 2 tools: get_gene, get_reference. Their descriptions and schemas cost roughly 252 tokens of context every time the server is loaded.

### Is the Pombase MCP server still maintained?

Pombase 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 Pombase MCP server under?

Pombase 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 Pombase MCP server?

VerifyMCP ran 16 checks on Pombase, 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-pombase
- Socket report: https://socket.dev/npm/package/@pipeworx/mcp-pombase
- Repository: https://github.com/pipeworx-io/mcp-pombase
- Website: https://pipeworx.io/packs/pombase
- Changelog RSS feed: https://verifymcp.io/servers/pipeworx-io-pombase/pipeworx-mcp-pombase.xml
- Changelog JSON feed: https://verifymcp.io/servers/pipeworx-io-pombase/pipeworx-mcp-pombase/changelog.json
- Trust report (JSON): https://verifymcp.io/servers/pipeworx-io-pombase/pipeworx-mcp-pombase.json
- HTML version of this page: https://verifymcp.io/servers/pipeworx-io-pombase/pipeworx-mcp-pombase