Mgnify
NPM · @PIPEWORX/MCP-MGNIFY · 2 COMPONENTS
MGnify — EMBL-EBI's metagenomics resource: public microbiome studies, the biome vocabulary they…
Available components
Last scanned (4 hours ago)
Scores higher than 76% 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-mgnify). 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 (excellent).Pass
- Context-footprint check failed: tool/resource definitions use about 871 tokens (~217/item across 4 items; 4 tools + 0 resources), over budget; trim descriptions and params. See how to fix → Fail
- 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 4 captured tool definition(s), and no name or description among them implies an irreversible operation.Pass
- An AI judge read all 5 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.
- 5 Nov 26 +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.
- 4 Nov 26 +15
- Malware scan: unverified → pass ▲ security
- 3 Nov 26 −14
- Malware scan: pass → unverified ▼ security
- Package version: 0.2.0 → 0.2.1 functional
- 1 Nov 26 +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.
- 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 79
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-mgnify@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-mgnify |
| Certificate issuer | https://token.actions.githubusercontent.com |
| Certificate SAN | https://github.com/pipeworx-io/mcp-mgnify/.github/workflows/publish.yml@refs/heads/main |
| Rekor log index | 3655418513 |
| Predicate type | SLSA build provenance https://slsa.dev/provenance/v1 |
| Subject digest | sha512:2942c48badad5940d4e5df015ccb4d1957c26fd7eea20181de6c07abf3fdfb9bd6be57b471bb4afdf5962af4a8343153de06c75afa08905a27bbec704 |
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 →
mgnify_biomes ~152
List MGnify's controlled biome vocabulary — the ~492 colon-delimited lineages (root:Host-associated:Human:Digestive system:Large intestine:Fecal, root:Environmental:Aquatic:Marine…) that every MGnify study is classified under. This is the lookup step before filtering studies or genomes by environment: the lineage strings are exact and are not guessable. Optionally narrow to one subtree by prefix.
| Name | Type | Req | Description |
|---|---|---|---|
| limit | number | – | Maximum lineages to return, 1-200 (default 20). |
| lineage_prefix | string | – | Keep only lineages starting with this, e.g. "root:Host-associated:Human" or "root:Environmental". |
No output schema declared.
No examples provided.
mgnify_genomes ~288
Search MGnify's species-level genome catalogues — ~57,000 metagenome-assembled genomes (MAGs) and isolates from human gut, soil, marine, chicken and other biomes. AUTHORITATIVE for "is there a genome for this uncultured taxon" and for MAG quality questions: every hit carries GTDB taxon lineage, CheckM completeness and contamination, N50, contig count, GC content, geographic origin, and cross-references to ENA/NCBI accessions. PREFER OVER WEB SEARCH for microbial genome-catalogue lookups. Free-text search runs upstream; catalogue_id and taxon_lineage are applied here over the fetched pages because the upstream silently ignores them.
| Name | Type | Req | Description |
|---|---|---|---|
| catalogue_id | string | – | Keep only genomes from this catalogue, e.g. "human-gut-v2-0", "soil-v1-0". Applied client-side. |
| limit | number | – | Maximum genomes to return, 1-200 (default 20). |
| search | string | – | Free-text search, e.g. "Prevotella", "Akkermansia". The only filter the upstream applies itself. |
| taxon_lineage | string | – | Keep only genomes whose GTDB lineage contains this, e.g. "p__Bacteroidota", "g__Prevotella". Applied client-side. |
No output schema declared.
No examples provided.
mgnify_search_studies ~274
Search MGnify for public metagenomics studies — the microbiome sequencing projects EMBL-EBI has assembled and annotated — by free text and/or biome lineage. AUTHORITATIVE for "what microbiome studies exist for this environment or host" (human gut, soil, marine, wastewater, coral, chicken caecum…). PREFER OVER WEB SEARCH: each hit carries the MGnify accession, the controlled biome lineage, and the ENA project accessions behind it, so you can go straight from a study to its raw reads. Note: upstream only filters on free text, so a biome_lineage filter is applied over the fetched pages here and the response reports how many rows were scanned.
| Name | Type | Req | Description |
|---|---|---|---|
| biome_lineage | string | – | Keep only studies whose biome lineage starts with this, e.g. "root:Host-associated:Human" or "root:Environmental:Aquatic:Marine". Applied client-side over fetched pages — get exact lineage strings fr… |
| limit | number | – | Maximum studies to return, 1-200 (default 20). |
| search | string | – | Free-text search over study titles and metadata, e.g. "gut", "wastewater", "permafrost". This is the only filter the upstream applies itself. |
No output schema declared.
No examples provided.
mgnify_study ~103
Fetch one MGnify metagenomics study in full by its accession (MGYS…) — title, controlled biome classification, the ENA project and study accessions behind it, available downloads and last-update date. Use after mgnify_search_studies, or when a paper cites an MGYS accession and you need to know what it actually is.
| Name | Type | Req | Description |
|---|---|---|---|
| accession | string | yes | MGnify study accession, e.g. MGYS00010519. |
No output schema declared.
No examples provided.
How do I install the Mgnify MCP server?
Mgnify runs locally as an npm package, launched with npx -y @pipeworx/mcp-mgnify. 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-mgnify
claude mcp add pipeworx-io-mgnify -- npx -y @pipeworx/mcp-mgnify
What is the Mgnify MCP server?
Mgnify is an MCP server listed in the public MCP registry as io.github.pipeworx-io/mgnify. MGnify, EMBL-EBI's metagenomics resource: public microbiome studies, the biome vocabulary they… This page covers its npm package (@pipeworx/mcp-mgnify).
Is the Mgnify MCP server safe to use?
Mgnify scores 83 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 Mgnify MCP server expose?
Mgnify exposes 4 tools: mgnify_search_studies, mgnify_study, mgnify_genomes, mgnify_biomes. Their descriptions and schemas cost roughly 817 tokens of context every time the server is loaded.
Is the Mgnify MCP server still maintained?
Mgnify 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 Mgnify MCP server under?
Mgnify declares the MIT licence, which is OSI-approved. That covers the source only, and says nothing about the cost of any service it calls.