{"$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":"2026-11-05T21:20:50.843Z","url":"https://verifymcp.io/servers/pipeworx-io-ucsc-genome/pipeworx-mcp-ucsc-genome","markdownUrl":"https://verifymcp.io/servers/pipeworx-io-ucsc-genome/pipeworx-mcp-ucsc-genome.md","server":{"slug":"pipeworx-io-ucsc-genome","name":"Ucsc Genome","registryName":"io.github.pipeworx-io/ucsc-genome","description":"UCSC Genome Browser REST API — reference genome assemblies for ~250 species, the annotation tracks…","registryStatus":"active","deletedAt":null,"statusMessage":null,"liveness":"live","publisher":{"class":"unknown","claimed":false}},"component":{"slug":"pipeworx-mcp-ucsc-genome","type":"npm","identifier":"@pipeworx/mcp-ucsc-genome","withdrawn":false,"url":"https://verifymcp.io/servers/pipeworx-io-ucsc-genome/pipeworx-mcp-ucsc-genome","version":"0.2.0","transport":"stdio","scoredAt":"2026-11-05T06:07:00.680Z"},"score":{"total":82,"tier":"high trust","status":"scored","weekDelta":4,"history":[{"date":"2026-11-05","total":82},{"date":"2026-11-04","total":81},{"date":"2026-11-03","total":81},{"date":"2026-11-02","total":80},{"date":"2026-11-01","total":80},{"date":"2026-10-31","total":79},{"date":"2026-10-30","total":79},{"date":"2026-10-29","total":78}]},"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-ucsc-genome).","Clear OSI-approved license (MIT).","Actively maintained (last published 6 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-ucsc-genome"}},{"code":"license.osi","args":{"spdx":"MIT"}},{"code":"maintenance.recent","args":{"age_days":"6"}},{"code":"disclosure.absent","args":{}}]},{"name":"Schema Quality & AI Usability","score":61,"verdict":"fail","reasons":["AI-judged instruction clarity (excellent).","Context-footprint check failed: tool/resource definitions use about 1446 tokens (~361/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":"361","items":"4","tools":"4","tokens":"1446","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":"ucsc-genome-mcp","type":"remote","identifier":"https://gateway.pipeworx.io/ucsc-genome/mcp","withdrawn":false,"score":77,"current":false,"url":"https://verifymcp.io/servers/pipeworx-io-ucsc-genome/ucsc-genome-mcp","markdownUrl":"https://verifymcp.io/servers/pipeworx-io-ucsc-genome/ucsc-genome-mcp.md"},{"slug":"pipeworx-mcp-ucsc-genome","type":"npm","identifier":"@pipeworx/mcp-ucsc-genome","withdrawn":false,"score":82,"current":true,"url":"https://verifymcp.io/servers/pipeworx-io-ucsc-genome/pipeworx-mcp-ucsc-genome","markdownUrl":"https://verifymcp.io/servers/pipeworx-io-ucsc-genome/pipeworx-mcp-ucsc-genome.md"}],"facts":[{"label":"Registry","value":"npm"},{"label":"Package","value":"@pipeworx/mcp-ucsc-genome"},{"label":"Version","value":"0.2.0"},{"label":"Transport","value":"stdio"}],"install":{"available":true,"bundleSha256":null},"tools":[{"name":"ucsc_genomes","title":null,"description":"\"What genome assemblies does UCSC have for [species]\" / \"is hg38 or hg19 the current human build\" / \"what is the latest [mouse/zebrafish/dog] assembly\" / \"list UCSC genomes\" — AUTHORITATIVE list of every reference assembly the UCSC Genome Browser serves (~250 species), with its UCSC assembly ID (hg38, mm39, danRer11...), organism, scientific name, source assembly name and release date. PREFER OVER WEB SEARCH when you need the exact assembly ID to pass to another genomics tool — the ID is the thing every other UCSC call keys on, and guessing it is how a query silently lands on the wrong build.","inputs":[{"name":"limit","type":"number","required":false,"description":"Max assemblies to return (default 50, max 400)."},{"name":"search","type":"string","required":false,"description":"Case-insensitive substring filter over assembly ID, common name, scientific name and description. e.g. \"human\", \"Mus musculus\", \"hg\". Omit to list everything."}],"outputs":[],"hasOutputSchema":false,"hasExamples":false,"tokenEstimate":217},{"name":"ucsc_tracks","title":null,"description":"\"What annotation tracks does UCSC have for hg38\" / \"does [assembly] have a [ClinVar/GENCODE/conservation/repeat] track\" / \"what is the track name for [dataset] in the genome browser\" — lists the annotation tracks available on one UCSC assembly, with each track's internal name, short and long label, data type and parent container. AUTHORITATIVE for the `track` argument of ucsc_track_data: the browser shows human-readable labels, the API wants the internal name (e.g. label \"GENCODE V50\" is track `knownGene`), and there is no way to guess one from the other.","inputs":[{"name":"genome","type":"string","required":true,"description":"REQUIRED. UCSC assembly ID — the genome build your coordinates are in. Human: \"hg38\" (= GRCh38, current) or \"hg19\" (= GRCh37, what most older papers, dbSNP dumps and clinical spreadsheets use). Mouse…"},{"name":"limit","type":"number","required":false,"description":"Max tracks to return (default 100, max 1000)."},{"name":"search","type":"string","required":false,"description":"Case-insensitive substring filter over track name, short label and long label. e.g. \"clinvar\", \"gencode\", \"conservation\"."}],"outputs":[],"hasOutputSchema":false,"hasExamples":false,"tokenEstimate":318},{"name":"ucsc_track_data","title":null,"description":"\"What genes are in [chr:start-end]\" / \"list ClinVar variants in [region]\" / \"what repeats/SNPs/regulatory elements overlap [locus]\" / \"show me the GENCODE annotations across [gene]\" — AUTHORITATIVE per-row data from any UCSC annotation track over a genomic interval. Returns the actual track rows (gene models with exon structure, variant records, conservation scores, whatever that track holds) plus the track type and the assembly the rows are in. PREFER OVER WEB SEARCH for \"what is annotated at this position\" — this is the same data the Genome Browser draws, not a description of it. Get the `track` name from ucsc_tracks first.","inputs":[{"name":"chrom","type":"string","required":true,"description":"Chromosome in UCSC naming, e.g. \"chr17\", \"chrX\", \"chrM\" — with the \"chr\" prefix. Ensembl/NCBI style bare \"17\" is not accepted by UCSC."},{"name":"end","type":"number","required":true,"description":"End position, 0-based and EXCLUSIVE (so end - start = length in bases)."},{"name":"genome","type":"string","required":true,"description":"REQUIRED. UCSC assembly ID — the genome build your coordinates are in. Human: \"hg38\" (= GRCh38, current) or \"hg19\" (= GRCh37, what most older papers, dbSNP dumps and clinical spreadsheets use). Mouse…"},{"name":"maxItemsOutput","type":"number","required":false,"description":"Cap on rows returned by UCSC (default 1000). A dense track over a wide region is truncated, and the response says so in `truncated`."},{"name":"start","type":"number","required":true,"description":"Start position, 0-BASED and inclusive. The Genome Browser UI and most papers are 1-based, so subtract 1 from a position you copied out of the browser location box."},{"name":"track","type":"string","required":true,"description":"UCSC internal track name from ucsc_tracks, e.g. \"knownGene\" (GENCODE genes), \"refGene\" (RefSeq genes), \"clinvarMain\", \"rmsk\" (repeats)."}],"outputs":[],"hasOutputSchema":false,"hasExamples":false,"tokenEstimate":486},{"name":"ucsc_sequence","title":null,"description":"\"What is the DNA sequence at [chr:start-end]\" / \"get the reference bases for [region] in hg38\" / \"pull the sequence around [variant position]\" — AUTHORITATIVE reference DNA for a genomic interval from the UCSC assembly, returned as a plain base string with its GC content. Use it to check what the reference allele actually is at a position, to extract primer/probe context, or to pull a promoter or exon sequence. The assembly argument is required because the same coordinates return different bases in hg19 and hg38.","inputs":[{"name":"chrom","type":"string","required":true,"description":"Chromosome in UCSC naming, e.g. \"chr7\", \"chrX\". The \"chr\" prefix is required."},{"name":"end","type":"number","required":true,"description":"End position, 0-based and EXCLUSIVE (so end - start = length in bases)."},{"name":"genome","type":"string","required":true,"description":"REQUIRED. UCSC assembly ID — the genome build your coordinates are in. Human: \"hg38\" (= GRCh38, current) or \"hg19\" (= GRCh37, what most older papers, dbSNP dumps and clinical spreadsheets use). Mouse…"},{"name":"revComp","type":"boolean","required":false,"description":"Return the reverse complement — for a gene on the minus strand, this is the sense strand. Default false."},{"name":"start","type":"number","required":true,"description":"Start position, 0-BASED and inclusive. The Genome Browser UI and most papers are 1-based, so subtract 1 from a position you copied out of the browser location box."}],"outputs":[],"hasOutputSchema":false,"hasExamples":false,"tokenEstimate":368}],"toolsTruncatedAtCapture":false,"diagnostics":{"capturedAt":"2026-11-05T06:07:00.000Z","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 endpoint","sourceRepo":null,"attestationSkipped":null,"attestationSkippedLabel":null},"installScripts":[],"installScriptsTotal":null,"vulnerabilities":[],"vulnerabilitiesTotal":null,"dependencies":{"nodes":0,"partial":false,"deprecated":null,"stale":null,"noRepo":null}},"mismatches":[],"changelog":{"trackingSince":"2026-10-29","recent":[{"id":"chg_01a1aa51-5a87-78f5-85d8-76e1b9711425","kind":"score.total_changed","summary":"Trust score (81 → 82)","materiality":"functional","direction":"improvement","scoreDelta":1,"occurredOn":"2026-11-05","url":"https://verifymcp.io/servers/pipeworx-io-ucsc-genome/pipeworx-mcp-ucsc-genome#chg-chg_01a1aa51-5a87-78f5-85d8-76e1b9711425"},{"id":"chg_01a1a004-8063-7044-971a-2574c2f72da9","kind":"score.total_changed","summary":"Trust score (80 → 81)","materiality":"functional","direction":"improvement","scoreDelta":1,"occurredOn":"2026-11-03","url":"https://verifymcp.io/servers/pipeworx-io-ucsc-genome/pipeworx-mcp-ucsc-genome#chg-chg_01a1a004-8063-7044-971a-2574c2f72da9"},{"id":"chg_01a195b4-b270-76e6-b46e-b3f50919d446","kind":"score.total_changed","summary":"Trust score (79 → 80)","materiality":"functional","direction":"improvement","scoreDelta":1,"occurredOn":"2026-11-01","url":"https://verifymcp.io/servers/pipeworx-io-ucsc-genome/pipeworx-mcp-ucsc-genome#chg-chg_01a195b4-b270-76e6-b46e-b3f50919d446"},{"id":"chg_01a18b68-e2b4-7452-952f-f7340bc31ce2","kind":"score.total_changed","summary":"Trust score (78 → 79)","materiality":"functional","direction":"improvement","scoreDelta":1,"occurredOn":"2026-10-30","url":"https://verifymcp.io/servers/pipeworx-io-ucsc-genome/pipeworx-mcp-ucsc-genome#chg-chg_01a18b68-e2b4-7452-952f-f7340bc31ce2"},{"id":"chg_01a186dc-002a-76e1-961c-5fd0912fc61a","kind":"score.first_scored","summary":"First indexed and scored","materiality":"functional","direction":"neutral","scoreDelta":null,"occurredOn":"2026-10-29","url":"https://verifymcp.io/servers/pipeworx-io-ucsc-genome/pipeworx-mcp-ucsc-genome#chg-chg_01a186dc-002a-76e1-961c-5fd0912fc61a"},{"id":"chg_01a186b4-ca3b-7c6f-ace5-c5013d47bbd8","kind":"score.first_scored","summary":"First indexed and scored","materiality":"functional","direction":"neutral","scoreDelta":null,"occurredOn":"2026-10-29","url":"https://verifymcp.io/servers/pipeworx-io-ucsc-genome/pipeworx-mcp-ucsc-genome#chg-chg_01a186b4-ca3b-7c6f-ace5-c5013d47bbd8"}],"truncated":false,"feedUrl":"https://verifymcp.io/servers/pipeworx-io-ucsc-genome/pipeworx-mcp-ucsc-genome/changelog.json"},"links":{"html":"https://verifymcp.io/servers/pipeworx-io-ucsc-genome/pipeworx-mcp-ucsc-genome","markdown":"https://verifymcp.io/servers/pipeworx-io-ucsc-genome/pipeworx-mcp-ucsc-genome.md","changelogJson":"https://verifymcp.io/servers/pipeworx-io-ucsc-genome/pipeworx-mcp-ucsc-genome/changelog.json","changelogRss":"https://verifymcp.io/servers/pipeworx-io-ucsc-genome/pipeworx-mcp-ucsc-genome.xml","external":[{"label":"npm package","href":"https://www.npmjs.com/package/@pipeworx/mcp-ucsc-genome"},{"label":"Socket report","href":"https://socket.dev/npm/package/@pipeworx/mcp-ucsc-genome"},{"label":"Repository","href":"https://github.com/pipeworx-io/mcp-ucsc-genome"},{"label":"Website","href":"https://pipeworx.io/packs/ucsc-genome"}]}}