Atlas / MCP servers / dbcls / togomcp

togomcpCAUTION

Name: togomcp
Author: dbcls

mcp/dbcls/togomcp

MCP server by dbcls · biomedical ai · knowledge graph · life sciences · Audited 2026-10-10

⚑ Report / re-scan Source ↗

MCP server for life-science knowledge graphs

Verdict

CAUTION

Grade

Trust score

80 /100

Exposed tools

5 5r · 0w · 0d

Transport

stdio · streamable-http

License

MIT

Stars

Overview

From the repository's own README, as read at the audited commit. Badges and raw HTML are left out.

An MCP (Model Context Protocol) server that gives AI assistants (Claude, etc.) access to biological and biomedical RDF databases via SPARQL at the RDF Portal, as well as selected REST APIs (NCBI E-utilities, UniProt, ChEMBL, PDB, Reactome, Rhea, MeSH, and more).

Quick Start: Remote Server (No Installation)

You can use the hosted TogoMCP server directly — no local setup needed. See https://togomcp.rdfportal.org/ for connection instructions.

Local Installation

Prerequisites

Python >= 3.11
uv package manager

1. Install `uv`

# macOS/Linux
curl -LsSf https://astral.sh/uv/install.sh | sh

# Windows (PowerShell)
powershell -ExecutionPolicy ByPass -c "irm https://astral.sh/uv/install.ps1 | iex"

2. Clone and install

git clone https://github.com/dbcls/togomcp.git
cd togomcp
uv sync

3. Set NCBI API Key (required for NCBI tools)

Obtain your NCBI API key and export it:

export NCBI_API_KEY="your-key-here"

Configuration

Claude Desktop

Edit your Claude Desktop config file:

macOS: ~/Library/Application Support/Claude/claude_desktop_config.json
Windows: ~\AppData\Roaming\Claude\claude_desktop_config.json

{
"mcpServers": {
"togomcp": {
"command": "/path/to/uv",
"args": [
"--directory",
"/path/to/togomcp",
"run",
"togo-mcp-local"
],
"env": {
"NCBI_API_KEY": "your-key-here"
}
}
}
}

Tip: Run which uv (macOS/Linux) or where uv (Windows) to find the full path

Read from source at commit 6933741f07e7OBSERVED · 2026-10-10

Connect

Built from this server's own package name, version and transport as found in its source — not copied from anyone's documentation, so it cannot drift against a page we do not control. Replace the environment placeholders with a token scoped to the least it needs.

claude-code

claude mcp add togo-mcp --env ANTHROPIC_API_KEY=${ANTHROPIC_API_KEY} --env ANTHROPIC_AUTH_TOKEN=${ANTHROPIC_AUTH_TOKEN} --env NCBI_API_KEY=${NCBI_API_KEY} --env TOGOMCP_STATS_PASSWORD=${TOGOMCP_STATS_PASSWORD} -- uvx togo-mcp

claude-desktop

{
  "mcpServers": {
    "togo-mcp": {
      "command": "uvx",
      "args": [
        "togo-mcp"
      ],
      "env": {
        "ANTHROPIC_API_KEY": "${ANTHROPIC_API_KEY}",
        "ANTHROPIC_AUTH_TOKEN": "${ANTHROPIC_AUTH_TOKEN}",
        "NCBI_API_KEY": "${NCBI_API_KEY}",
        "TOGOMCP_STATS_PASSWORD": "${TOGOMCP_STATS_PASSWORD}"
      }
    }
  }
}

Exposed tools (5)

5 read · 0 write · 0 destructive.

Tool	Risk	Description
`TogoMCP_Usage_Guide`	read
`get_compound_attributes_from_pubchem`	read
`get_pubchem_compound_id`	read
`get_sparql_endpoints`	read	Get the available SPARQL endpoints for RDF Portal.
`mie-refresh`	read	Batch-build/revise MIE files (one mie-builder agent per database), then independently re-validate each against the live endpoint

Trust audit

CAUTIONgrade B · trust 80/100 Install with care. The audit found things worth knowing before you trust its output.

Layer	What it checks	Result
L0	Provenance & inventory	WARN
L1	Static analysis of the code	WARN
L2	Instruction surface (what it tells the agent)	PASS
L3	Class-specific surface	PASS
L4	Behavioural (sandbox)	SKIPPED

What the source does

Filesystem: declared (2 observation(s))
Network: declared (9 observation(s))
Shell: none-observed
Dependencies: pinned
Secrets in source: none-found

Findings (25)

MEDIUMInventory / provenance · inv.symlink · CWE-1104

.claude/skills/disease-analysis

.claude/skills/disease-analysis

Why it matters. link not followed

MEDIUMInventory / provenance · inv.symlink · CWE-1104

.claude/skills/prism

.claude/skills/prism

Why it matters. link not followed

MEDIUMInventory / provenance · inv.symlink · CWE-1104

.claude/skills/research-article-analysis

.claude/skills/research-article-analysis

Why it matters. link not followed

MEDIUMInformation disclosure · disclose.log_secret · CWE-209, CWE-532

scripts/check_mie_leakage.py:260

print(f"  !  STALE waiver {w['question']} / {w['database']} / {w['token']!r} "

MEDIUMNetwork egress · net.raw_ip · CWE-200, CWE-319

.claude/skills/benchmark-runner/scripts/run_benchmark.py:132

f"http://127.0.0.1:{port}/mcp", headers={"Accept": "text/event-stream"}), timeout=5)

MEDIUMNetwork egress · net.raw_ip · CWE-200, CWE-319

.claude/skills/benchmark-runner/scripts/run_benchmark.py:240

url = PRODUCTION_URL if args.target == "production" else f"http://127.0.0.1:{args.port}/mcp"

MEDIUMNetwork egress · net.raw_ip · CWE-200, CWE-319

scripts/deploy.sh:134

code=$(curl -s -o /dev/null -w '%{http_code}' -H "Host: $host" "http://127.0.0.1:${port}/" 2>/dev/null || true)

LOWFilesystem / path · fs.traversal · CWE-22, CWE-59

benchmark/studies/conditions/run_conditions.py:185

help="question YAML paths (default: all ../../questions/question_*.yaml)")

LOWFilesystem / path · fs.traversal · CWE-22, CWE-59

tests/test_kegg.py:748

await pathway_neighborhood(pathway=MAP, seeds="../../get/hsa:207")

LOWFilesystem / path · fs.traversal · CWE-22, CWE-59

tests/test_workflows.py:163

"bad", ["../SKILL.md", "/etc/passwd", "references/../../x.md", "references/x.py", "C:\\x.md"]

LOWNetwork egress · net.raw_ip · CWE-200, CWE-319

benchmark/studies/ablation/run_ablation.py:228

url = f"http://127.0.0.1:{port}/mcp"

LOWNetwork egress · net.raw_ip · CWE-200, CWE-319

benchmark/studies/ablation/run_ablation.py:296

servers["togomcp"] = {"type": "http", "url": f"http://127.0.0.1:{port}/mcp"}

LOWObfuscation / stealth · obf.decode_call · CWE-506, CWE-94

togo_mcp/server.py:1115

decoded = _base64.b64decode(header[6:]).decode("utf-8")

LOWObfuscation / stealth · obf.homoglyph · CWE-506, CWE-94

benchmark/studies/ablation/ablation_analysis.py:552

hdr += f" {'Δsparql':>8s} {'±95%CI':>7s} {'Δcost$':>7s}"

LOWObfuscation / stealth · obf.homoglyph · CWE-506, CWE-94

benchmark/studies/ablation/ablation_analysis.py:554

hdr += f" {'Δcorr':>7s}"

LOWObfuscation / stealth · obf.homoglyph · CWE-506, CWE-94

benchmark/studies/conditions/conditions_analysis.py:166

f"Δvs {REFERENCE}: {_fmt(delta, '+.2f')}")

LOWPrompt injection · prompt.transfer_instruction · CWE-94, CWE-1427

togo_mcp/data/docs/togomcp-intro.html:1630

<llm-meta-widget llm-url="https://hub.aibranch.org" tool-hub-url="https://hub.aibranch.org" model="qwen3-8-27b-fast" hub-tools="TogoMCP" default-hub-tools="TogoMCP" auth-required="false" enable-model-

Why it matters. an instruction to move sensitive data to an outside destination

Fix. remove; a skill never needs the user's secrets off the machine

LOWPrompt injection · prompt.transfer_instruction · CWE-94, CWE-1427

togo_mcp/data/resources/usage_guide_v7/02b_database_catalog.md:81

**Not an RDF Portal database — KEGG.** `database="kegg"` is invalid on `run_sparql` and `get_MIE_file`: KEGG has no SPARQL endpoint and no MIE. The `kegg_*` tools exist only on a local stdio server wh

Why it matters. an instruction to move sensitive data to an outside destination

Fix. remove; a skill never needs the user's secrets off the machine

LOWPrompt injection · prompt.transfer_instruction · CWE-94, CWE-1427

togo_mcp/data/resources/usage_guide_v7/references/database-catalog.md:134

**Check your tool list before offering KEGG to the user.** KEGG is OFF BY DEFAULT. The `kegg_*` tools appear only on the local stdio server (`togo-mcp-local`) AND only when the operator sets `TOGOMCP_

Why it matters. an instruction to move sensitive data to an outside destination

Fix. remove; a skill never needs the user's secrets off the machine