Wikipathways
NPM · @PIPEWORX/MCP-WIKIPATHWAYS · 2 COMPONENTS
WikiPathways MCP — open community pathway database.
Available components
Last scanned (2 hours ago)
Scores higher than 81% 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-wikipathways). View diagnostics → Pass
- Clear OSI-approved license (MIT).Pass
- Actively maintained (last published 7 days ago).Pass
- Disclosure check failed: no security disclosure policy was found in the source repository. See how to fix → Fail
Schema Quality & AI Usability76
- AI-judged instruction clarity (good).Pass
- Tool/resource definitions use about 380 tokens (~126/item across 3 items; 3 tools + 0 resources), lean.Pass
- Usage-examples check failed: none of the tools include examples. See how to fix → Fail
Stability & Change Management23
- Stability observed for 7 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 3 captured tool definition(s), and no name or description among them implies an irreversible operation.Pass
- An AI judge read all 4 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 +1
No change was recorded against any check on this day. Stability & Change Management went from 17 to 20. That category is still filling its 30-day observation window: 5 days of observed history at the previous scan, 6 at this one. The score rises as the window fills, whether or not the server changes.
- 2 Nov 26 +1
No change was recorded against any check on this day. Stability & Change Management went from 10 to 13. That category is still filling its 30-day observation window: 3 days of observed history at the previous scan, 4 at this one. The score rises as the window fills, whether or not the server changes.
- 30 Oct 26 +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.
- 29 Oct 26 81
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-wikipathways@0.2.0
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-wikipathways |
| Certificate issuer | https://token.actions.githubusercontent.com |
| Certificate SAN | https://github.com/pipeworx-io/mcp-wikipathways/.github/workflows/publish.yml@refs/heads/main |
| Rekor log index | 3561111109 |
| Predicate type | SLSA build provenance https://slsa.dev/provenance/v1 |
| Subject digest | sha512:687d29a65c9cc903a133c05d82f43289c157fd0837dd4c537a84eeddf7d77d14f4e0b131d68df3b28a5d7b2975d17b4a2f25feb951ae855bec70a1c49 |
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 →
get_pathway ~69
Get metadata and a viewer link for one WikiPathways pathway by its WikiPathways id (e.g. "WP554"). Returns name, species, revision, and a human-viewable diagram URL. Keyless.
| Name | Type | Req | Description |
|---|---|---|---|
| id | string | yes | A WikiPathways id like "WP554". |
No output schema declared.
No examples provided.
list_pathways ~106
List all WikiPathways pathways for a single organism. Give a Latin or common name, e.g. "Homo sapiens", "human", or "mouse". Returns each pathway's id, name, link, and last revision. Keyless.
| Name | Type | Req | Description |
|---|---|---|---|
| limit | number | – | Max results (default 50, max 200). |
| organism | string | yes | Organism by Latin or common name, e.g. "Homo sapiens", "human", "mouse". |
No output schema declared.
No examples provided.
search_pathways ~149
Search WikiPathways (open community pathway database) for biological pathways by name. Pathways map genes/proteins/metabolites in processes like glycolysis, apoptosis, or signaling. Optionally restrict to one organism by Latin or common name. Keyless. Complements KEGG/Reactome.
| Name | Type | Req | Description |
|---|---|---|---|
| limit | number | – | Max results (default 25, max 100). |
| organism | string | – | Optional. Restrict to an organism by Latin or common name, e.g. "Homo sapiens" or "human". |
| query | string | yes | Text to match in the pathway name (case-insensitive), e.g. "glycolysis", "apoptosis". |
No output schema declared.
No examples provided.
How do I install the Wikipathways MCP server?
Wikipathways runs locally as an npm package, launched with npx -y @pipeworx/mcp-wikipathways. 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-wikipathways
claude mcp add pipeworx-io-wikipathways -- npx -y @pipeworx/mcp-wikipathways
What is the Wikipathways MCP server?
Wikipathways is an MCP server listed in the public MCP registry as io.github.pipeworx-io/wikipathways. WikiPathways MCP, open community pathway database. This page covers its npm package (@pipeworx/mcp-wikipathways).
Is the Wikipathways MCP server safe to use?
Wikipathways 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 Wikipathways MCP server expose?
Wikipathways exposes 3 tools: search_pathways, list_pathways, get_pathway. Their descriptions and schemas cost roughly 324 tokens of context every time the server is loaded.
Is the Wikipathways MCP server still maintained?
Wikipathways 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 Wikipathways MCP server under?
Wikipathways declares the MIT licence, which is OSI-approved. That covers the source only, and says nothing about the cost of any service it calls.