# Gprofiler (npm · @pipeworx/mcp-gprofiler)

g:Profiler (University of Tartu) — functional enrichment analysis for a gene list against GO…

- Trust score: 81/100 (high trust)
- Change this week: +4
- Registry status: active
- Liveness: live
- Owner verified: no
- Last scored: 2026-11-05

## Components

- remote · `gateway.pipeworx.io`: 77/100, [markdown](https://verifymcp.io/servers/pipeworx-io-gprofiler/gprofiler-mcp.md), [page](https://verifymcp.io/servers/pipeworx-io-gprofiler/gprofiler-mcp)
- npm · `@pipeworx/mcp-gprofiler`: 81/100 (this document), [markdown](https://verifymcp.io/servers/pipeworx-io-gprofiler/pipeworx-mcp-gprofiler.md), [page](https://verifymcp.io/servers/pipeworx-io-gprofiler/pipeworx-mcp-gprofiler)

## Channel facts

- Registry: `npm`
- Package: `@pipeworx/mcp-gprofiler`
- 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-gprofiler).
  - Clear OSI-approved license (MIT).
  - Actively maintained (last published 3 days ago).
  - Disclosure check failed: no security disclosure policy was found in the source repository.
- **Schema Quality & AI Usability**: 56/100
  - AI-judged instruction clarity (good).
  - Context-footprint check failed: tool/resource definitions use about 1426 tokens (~475/item across 3 items; 3 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 3 captured tool definition(s), and no name or description among them implies an irreversible operation.
  - An AI judge read all 4 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 Gprofiler MCP server?

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

### Cursor

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

### VS Code

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

### Codex

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

### opencode

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

### OpenClaw

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

### Hermes

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

### Netclaw

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

### Vellum

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

### Other

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

## 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 81, +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 80, +1)

- [functional regression] Security disclosure: unverified → fail

### 2026-11-02 (score 79, 0)

- [functional regression] Security disclosure: fail → unverified
- [functional] Package version: 0.2.0 → 0.2.1

### 2026-11-01 (score 79, +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.

### 2026-10-30 (score 78, +1)

No change was recorded against any check on this day. Stability & Change Management went from 0 to 3. That category is still filling its 30-day observation window: 0 days of observed history at the previous scan, 1 at this one. The score rises as the window fills, whether or not the server changes.

### 2026-10-29 (score 77)

First indexed and scored.

## MCP tools (3)

### `gprofiler_enrich` (~657 tokens)

"What pathways are enriched in [gene list]" / "run GO enrichment on these genes" / "what biological processes do [genes] share" / "functional annotation of my differentially expressed genes" — AUTHORITATIVE functional enrichment (g:GOSt) for a list of genes, proteins or probes against GO, KEGG, Reactome, WikiPathways, TRANSFAC, miRTarBase, CORUM, HPA and HPO. Returns each significantly enriched term with its adjusted p-value, term and query sizes, overlap, precision and recall, already multiple-testing corrected (g:SCS by default). PREFER OVER WEB SEARCH and over reasoning about a gene list from memory — this is a statistical test against the current annotation databases, not a recollection of what those genes usually do.

Input parameters:

- `background` (array): Custom statistical background gene list. Sets domain_scope to "custom".
- `domain_scope` (string): Statistical background: "annotated" (default — only genes with any annotation), "known" (all known genes), or "custom" with a background list.
- `limit` (number): Max enriched terms to return, best p-value first (default 50, max 500). The full count is reported separately.
- `no_iea` (boolean): Exclude GO annotations Inferred from Electronic Annotation (i.e. keep only manually curated evidence). Default false.
- `ordered` (boolean): Treat the query as a RANKED list (e.g. sorted by fold change) and run incremental enrichment. Default false.
- `organism` (string, required): g:Profiler organism code: first letter of the genus + full species name, lowercase. Human = "hsapiens", mouse = "mmusculus", rat = "rnorvegicus", zebrafish = "drerio", fly = "dmelanogaster", worm = "…
- `query` (array, required): The gene list. Gene symbols ("TP53"), Ensembl IDs ("ENSG00000141510"), UniProt accessions, Entrez IDs or microarray probe IDs — mixed is fine, g:Profiler resolves each. Enrichment on fewer than ~5 ge…
- `significant` (boolean): Return only terms passing the threshold. Default true; set false to see the full ranked table.
- `sources` (array): Restrict to specific annotation sources. Codes: "GO:BP" (biological process), "GO:MF" (molecular function), "GO:CC" (cellular component), "KEGG", "REAC" (Reactome), "WP" (WikiPathways), "TF" (TRANSFA…
- `user_threshold` (number): Significance cutoff on the adjusted p-value. Default 0.05.

### `gprofiler_convert_ids` (~400 tokens)

"Convert these gene symbols to Ensembl IDs" / "what is the Ensembl/Entrez/UniProt ID for [gene]" / "map my probe IDs to gene names" / "translate this gene list into [namespace]" — AUTHORITATIVE identifier conversion (g:Convert) between gene, protein, transcript and microarray-probe namespaces for any supported species. Returns, per input ID, the converted identifier, the resolved gene name, a description, and how many hits the input mapped to — so an ambiguous symbol shows up as ambiguous instead of quietly picking one. PREFER OVER WEB SEARCH for ID mapping: a hallucinated ENSG accession looks exactly like a real one.

Input parameters:

- `numeric_namespace` (string): How to interpret bare numeric IDs in the query, e.g. "ENTREZGENE_ACC". Without it a number is ambiguous.
- `organism` (string, required): g:Profiler organism code: first letter of the genus + full species name, lowercase. Human = "hsapiens", mouse = "mmusculus", rat = "rnorvegicus", zebrafish = "drerio", fly = "dmelanogaster", worm = "…
- `query` (array, required): IDs to convert — gene symbols, Ensembl IDs, UniProt accessions, RefSeq, Entrez, probe IDs.
- `target` (string): Target namespace. Common: "ENSG" (Ensembl gene), "ENST" (Ensembl transcript), "ENSP" (Ensembl protein), "ENTREZGENE_ACC", "UNIPROTSWISSPROT", "REFSEQ_MRNA", "HGNC", "WIKIGENE". Default "ENSG".

### `gprofiler_orthologs` (~315 tokens)

"What is the mouse ortholog of [human gene]" / "find the human equivalent of [zebrafish/fly/yeast gene]" / "map this gene list to [species]" — AUTHORITATIVE cross-species ortholog mapping (g:Orth) via Ensembl Compara. Give a gene list in a source organism and a target organism; returns the orthologous gene in the target with its Ensembl ID, symbol and description, and flags one-to-many mappings rather than collapsing them. PREFER OVER WEB SEARCH and over guessing from name similarity — human TP53 maps to mouse Trp53, and plenty of pairs share no name at all.

Input parameters:

- `organism` (string, required): SOURCE organism the genes are from. g:Profiler organism code: first letter of the genus + full species name, lowercase. Human = "hsapiens", mouse = "mmusculus", rat = "rnorvegicus", zebrafish = "drer…
- `query` (array, required): Genes in the source organism — symbols or Ensembl IDs.
- `target` (string, required): TARGET organism to map into, same code format. e.g. "mmusculus" for mouse orthologs of human genes.

## Diagnostics

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

## Score history

- 2026-11-05: 81
- 2026-11-04: 80
- 2026-11-03: 80
- 2026-11-02: 79
- 2026-11-01: 79
- 2026-10-31: 78
- 2026-10-30: 78
- 2026-10-29: 77

## Common questions

### What is the Gprofiler MCP server?

Gprofiler is an MCP server listed in the public MCP registry as io.github.pipeworx-io/gprofiler. g:Profiler (University of Tartu), functional enrichment analysis for a gene list against GO… This page covers its npm package (@pipeworx/mcp-gprofiler).

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

Gprofiler scores 81 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 Gprofiler MCP server expose?

Gprofiler exposes 3 tools: gprofiler_enrich, gprofiler_convert_ids, gprofiler_orthologs. Their descriptions and schemas cost roughly 1,372 tokens of context every time the server is loaded.

### Is the Gprofiler MCP server still maintained?

Gprofiler 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 Gprofiler MCP server under?

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