{"$schema":"https://verifymcp.io/schemas/trust-report.json","schemaVersion":1,"license":{"name":"CC BY-NC 4.0","url":"https://creativecommons.org/licenses/by-nc/4.0/"},"generatedAt":"2026-11-05T19:24:53.404Z","url":"https://verifymcp.io/servers/pipeworx-io-mgnify/pipeworx-mcp-mgnify","markdownUrl":"https://verifymcp.io/servers/pipeworx-io-mgnify/pipeworx-mcp-mgnify.md","server":{"slug":"pipeworx-io-mgnify","name":"Mgnify","registryName":"io.github.pipeworx-io/mgnify","description":"MGnify — EMBL-EBI's metagenomics resource: public microbiome studies, the biome vocabulary they…","registryStatus":"active","deletedAt":null,"statusMessage":null,"liveness":"live","publisher":{"class":"unknown","claimed":false}},"component":{"slug":"pipeworx-mcp-mgnify","type":"npm","identifier":"@pipeworx/mcp-mgnify","withdrawn":false,"url":"https://verifymcp.io/servers/pipeworx-io-mgnify/pipeworx-mcp-mgnify","version":"0.2.1","transport":"stdio","scoredAt":"2026-11-05T09:41:07.151Z"},"score":{"total":83,"tier":"high trust","status":"scored","weekDelta":4,"history":[{"date":"2026-11-05","total":83},{"date":"2026-11-04","total":82},{"date":"2026-11-03","total":67},{"date":"2026-11-02","total":81},{"date":"2026-11-01","total":81},{"date":"2026-10-31","total":80},{"date":"2026-10-30","total":80},{"date":"2026-10-29","total":79}]},"categories":[{"name":"Supply Chain Security","score":100,"verdict":"pass","reasons":["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."],"codes":[{"code":"supplychain.malware_clean","args":{}},{"code":"cve.none","args":{}},{"code":"installscript.none","args":{}},{"code":"dephealth.no_dependencies","args":{"deps":"0","unhealthy":"0"}}]},{"name":"Provenance & Transparency","score":97,"verdict":"fail","reasons":["Source repository is publicly reachable at the declared URL.","Cryptographically verified build provenance (signed, bound to pipeworx-io/mcp-mgnify).","Clear OSI-approved license (MIT).","Actively maintained (last published 2 days ago).","Disclosure check failed: no security disclosure policy was found in the source repository."],"codes":[{"code":"provenance.repo_verified","args":{}},{"code":"provenance.verified","args":{"repo":"pipeworx-io/mcp-mgnify"}},{"code":"license.osi","args":{"spdx":"MIT"}},{"code":"maintenance.recent","args":{"age_days":"2"}},{"code":"disclosure.absent","args":{}}]},{"name":"Schema Quality & AI Usability","score":67,"verdict":"fail","reasons":["AI-judged instruction clarity (excellent).","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.","Usage-examples check failed: none of the tools include examples."],"codes":[{"code":"schema.ai_quality","args":{"band":"excellent"}},{"code":"schema.footprint_heavy","args":{"avg":"217","items":"4","tools":"4","tokens":"871","resources":"0"}},{"code":"schema.examples_absent","args":{}}]},{"name":"Stability & Change Management","score":23,"verdict":"partial","reasons":["Stability observed for 7 of 30 days with no destabilising changes; credit accrues until the full window elapses."],"codes":[{"code":"stability.building_history","args":{"days":"7"}}]},{"name":"Tool Coverage","score":100,"verdict":"pass","reasons":["100% of tools have a non-trivial description (not blank, and not just the tool's name).","100% of tool parameters carry a description."],"codes":[{"code":"toolquality.descriptions","args":{"pct":"100"}},{"code":"toolquality.param_docs","args":{"pct":"100"}}]},{"name":"Tool Safety","score":100,"verdict":"pass","reasons":["No prompt-injection markers were found in the server instructions, tool names or descriptions we captured.","We read all 4 captured tool definition(s), and no name or description among them implies an irreversible operation.","An AI judge read all 5 captured unit(s) of tool text and found none that tries to manipulate the model reading it."],"codes":[{"code":"toolsafety.injection_clean","args":{}},{"code":"toolsafety.destructive_none","args":{"tools":"4"}},{"code":"toolsafety.manipulation_clean","args":{"units":"5","judged":"5"}}]},{"name":"Capabilities","score":100,"verdict":"pass","reasons":["Implements a supported MCP spec version (2025-11-25); the latest is 2026-07-28."],"codes":[{"code":"protocol.supported","args":{"latest":"2026-07-28","version":"2025-11-25"}}]}],"inconclusive":[],"malware":[],"components":[{"slug":"mgnify-mcp","type":"remote","identifier":"https://gateway.pipeworx.io/mgnify/mcp","withdrawn":false,"score":63,"current":false,"url":"https://verifymcp.io/servers/pipeworx-io-mgnify/mgnify-mcp","markdownUrl":"https://verifymcp.io/servers/pipeworx-io-mgnify/mgnify-mcp.md"},{"slug":"pipeworx-mcp-mgnify","type":"npm","identifier":"@pipeworx/mcp-mgnify","withdrawn":false,"score":83,"current":true,"url":"https://verifymcp.io/servers/pipeworx-io-mgnify/pipeworx-mcp-mgnify","markdownUrl":"https://verifymcp.io/servers/pipeworx-io-mgnify/pipeworx-mcp-mgnify.md"}],"facts":[{"label":"Registry","value":"npm"},{"label":"Package","value":"@pipeworx/mcp-mgnify"},{"label":"Version","value":"0.2.1"},{"label":"Transport","value":"stdio"}],"install":{"available":true,"bundleSha256":null},"tools":[{"name":"mgnify_search_studies","title":null,"description":"Search MGnify for public metagenomics studies — the microbiome sequencing projects EMBL-EBI has assembled and annotated — by free text and/or biome lineage. 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Free-text search runs upstream; catalogue_id and taxon_lineage are applied here over the fetched pages because the upstream silently ignores them.","inputs":[{"name":"catalogue_id","type":"string","required":false,"description":"Keep only genomes from this catalogue, e.g. \"human-gut-v2-0\", \"soil-v1-0\". Applied client-side."},{"name":"limit","type":"number","required":false,"description":"Maximum genomes to return, 1-200 (default 20)."},{"name":"search","type":"string","required":false,"description":"Free-text search, e.g. \"Prevotella\", \"Akkermansia\". The only filter the upstream applies itself."},{"name":"taxon_lineage","type":"string","required":false,"description":"Keep only genomes whose GTDB lineage contains this, e.g. \"p__Bacteroidota\", \"g__Prevotella\". 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Optionally narrow to one subtree by prefix.","inputs":[{"name":"limit","type":"number","required":false,"description":"Maximum lineages to return, 1-200 (default 20)."},{"name":"lineage_prefix","type":"string","required":false,"description":"Keep only lineages starting with this, e.g. \"root:Host-associated:Human\" or \"root:Environmental\"."}],"outputs":[],"hasOutputSchema":false,"hasExamples":false,"tokenEstimate":152}],"toolsTruncatedAtCapture":false,"diagnostics":{"capturedAt":"2026-11-05T09:41:07.000Z","track":"package","endpoint":null,"declaredUrl":null,"truncated":false,"tls":null,"dnssec":null,"auth":null,"httpsRedirect":null,"transports":[],"provenance":{"outcome":"verified","label":"Verified","reason":"verified","reasonLabel":"Verified","discovery":"attestation_endpoint","discoveryLabel":"Registry attestation 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