Monarch Initiative
NPM · @PIPEWORX/MCP-MONARCH-INITIATIVE · 2 COMPONENTS
Monarch Initiative MCP — biomedical knowledge graph.
Available components
Last scanned (12 hours ago)
Scores higher than 69% 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-monarch-initiative). View diagnostics → Pass
- Clear OSI-approved license (MIT).Pass
- Actively maintained (last published 2 days ago).Pass
- Disclosure check failed: no security disclosure policy was found in the source repository. See how to fix → Fail
Schema Quality & AI Usability67
- AI-judged instruction clarity (good).Pass
- Tool/resource definitions use about 397 tokens (~79/item across 5 items; 5 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 Coverage81
- 100% of tools have a non-trivial description (not blank, and not just the tool's name).Pass
- 42% of tool parameters carry a description.Partial
Tool Safety100
- No prompt-injection markers were found in the server instructions, tool names or descriptions we captured.Pass
- We read all 5 captured tool definition(s), and no name or description among them implies an irreversible operation.Pass
- An AI judge read all 6 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
Checks we ran (16)
- Malware scan
- Known CVEs
- Install scripts
- Dependency health
- Source repository
- Provenance
- License
- Maintenance
- Security disclosure
- Schema quality
- Stability
- Tool coverage
- Injection markers
- Destructive annotations
- Judged manipulation
- MCP protocol
Does not apply to this package (2)
- Endpoint SecurityScored on hosted endpoints only. A package has no live endpoint of its own for us to probe.
- Transport & ReachabilityScored on hosted endpoints only. A package has no live endpoint of its own for us to probe.
The score does not measure everything. What the score does not measure →
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 +16
- Malware scan: unverified → pass ▲ security
- 3 Nov 26 −13
- Malware scan: pass → unverified ▼ security
- Stability: unverified → 0.17 ▲ functional
- Package version: 0.2.0 → 0.2.1 functional
- 30 Oct 26 0
- Security disclosure: unverified → fail ▼ functional
- 29 Oct 26 78
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-monarch-initiative@0.2.1
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-monarch-initiative |
| Certificate issuer | https://token.actions.githubusercontent.com |
| Certificate SAN | https://github.com/pipeworx-io/mcp-monarch-initiative/.github/workflows/publish.yml@refs/heads/main |
| Rekor log index | 3655530447 |
| Predicate type | SLSA build provenance https://slsa.dev/provenance/v1 |
| Subject digest | sha512:09bcbcfece0cfbe6109565a9cd1d27c0599517b29b49acb54afc61d61306779ee486539bfa726b23c040addec7d0722faacfa2ef37a7fef34c481ce07 |
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 →
associations ~136
Fetch biolink associations (edges) involving a Monarch entity by its CURIE ID (e.g. MONDO:0007947); filter by association category (e.g. biolink:DiseaseToPhenotypicFeatureAssociation), predicate, or direction (subject/object/both).
| Name | Type | Req | Description |
|---|---|---|---|
| category | string | – | e.g. "biolink:DiseaseToPhenotypicFeatureAssociation" |
| direction | string | – | subject (default) | object | both |
| entity_id | string | yes | – |
| limit | number | – | – |
| predicate | string | – | e.g. "biolink:has_phenotype" |
No output schema declared.
No examples provided.
entity ~31
Single node by curie (e.g. "MONDO:0007947").
| Name | Type | Req | Description |
|---|---|---|---|
| id | string | yes | – |
No output schema declared.
No examples provided.
gene_to_disease ~36
Diseases associated with a gene (NCBIGene:… or HGNC:… id).
| Name | Type | Req | Description |
|---|---|---|---|
| gene_id | string | yes | – |
No output schema declared.
No examples provided.
phenotype_to_gene ~28
Genes annotated to a phenotype (HP:… id).
| Name | Type | Req | Description |
|---|---|---|---|
| phenotype_id | string | yes | – |
No output schema declared.
No examples provided.
search ~111
Full-text search across the Monarch biomedical knowledge graph for diseases, genes, phenotypes, and other biolink entities by query string; filter by category (e.g. biolink:Disease) and paginate with limit/offset.
| Name | Type | Req | Description |
|---|---|---|---|
| category | string | – | biolink:Disease | biolink:Gene | biolink:PhenotypicFeature | … |
| limit | number | – | 1-500 (default 20) |
| offset | number | – | – |
| query | string | yes | – |
No output schema declared.
No examples provided.
How do I install the Monarch Initiative MCP server?
Monarch Initiative runs locally as an npm package, launched with npx -y @pipeworx/mcp-monarch-initiative. 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-monarch-initiative
claude mcp add pipeworx-io-monarch-initiative -- npx -y @pipeworx/mcp-monarch-initiative
What is the Monarch Initiative MCP server?
Monarch Initiative is an MCP server listed in the public MCP registry as io.github.pipeworx-io/monarch-initiative. Monarch Initiative MCP, biomedical knowledge graph. This page covers its npm package (@pipeworx/mcp-monarch-initiative).
Is the Monarch Initiative MCP server safe to use?
Monarch Initiative 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 Monarch Initiative MCP server expose?
Monarch Initiative exposes 5 tools: search, entity, associations, phenotype_to_gene, gene_to_disease. Their descriptions and schemas cost roughly 342 tokens of context every time the server is loaded.
Is the Monarch Initiative MCP server still maintained?
Monarch Initiative 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 Monarch Initiative MCP server under?
Monarch Initiative 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 Monarch Initiative MCP server?
VerifyMCP ran 16 checks on Monarch Initiative, 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.