{"$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":"2026-11-05T23:39:09.579Z","url":"https://verifymcp.io/servers/trentleslie-biomapper/biomapper","markdownUrl":"https://verifymcp.io/servers/trentleslie-biomapper/biomapper.md","server":{"slug":"trentleslie-biomapper","name":"BioMapper","registryName":"io.github.trentleslie/biomapper","description":"Resolve metabolite, lipid, protein, gene and lab names to knowledge-graph IDs.","registryStatus":"active","deletedAt":null,"statusMessage":null,"liveness":"live","publisher":{"class":"unknown","claimed":false}},"component":{"slug":"biomapper","type":"pypi","identifier":"biomapper","withdrawn":false,"url":"https://verifymcp.io/servers/trentleslie-biomapper/biomapper","version":"1.6.2","transport":"stdio","scoredAt":"2026-11-05T00:45:30.877Z"},"score":{"total":52,"tier":"low","status":"scored","weekDelta":null,"history":[{"date":"2026-11-05","total":52}]},"categories":[{"name":"Supply Chain Security","score":50,"verdict":"partial","reasons":["Malware scan not yet available for this package.","No known CVEs affecting this package version or its production dependencies.","Runs poetry.core.masonry.api at install time, a recognised build step with no custom scripting around it.","2 of 33 dependencies flagged as unhealthy."],"codes":[{"code":"supplychain.malware_inconclusive","args":{"reason":"vendor_no_verdict"}},{"code":"cve.none","args":{}},{"code":"installscript.allowlisted","args":{"tool":"poetry.core.masonry.api","hooks":"build_backend"}},{"code":"dephealth.assessed","args":{"deps":"33","unhealthy":"2"}}]},{"name":"Provenance & Transparency","score":45,"verdict":"fail","reasons":["Source repository is publicly reachable at the declared URL.","Build provenance not yet verified.","Clear OSI-approved license (MIT).","Actively maintained (last published 0 days ago).","Disclosure check failed: no security disclosure policy was found in the source repository."],"codes":[{"code":"provenance.repo_verified","args":{}},{"code":"provenance.inconclusive","args":{"reason":"attestation_fetch_failed"}},{"code":"license.osi","args":{"spdx":"MIT"}},{"code":"maintenance.recent","args":{"age_days":"0"}},{"code":"disclosure.absent","args":{}}]},{"name":"Schema Quality & AI Usability","score":69,"verdict":"fail","reasons":["AI-judged instruction clarity (good).","Tool/resource definitions use about 843 tokens (~84/item across 10 items; 10 tools + 0 resources), lean.","Usage-examples check failed: none of the tools include examples."],"codes":[{"code":"schema.ai_quality","args":{"band":"good"}},{"code":"schema.footprint_lean","args":{"avg":"84","items":"10","tools":"10","tokens":"843","resources":"0"}},{"code":"schema.examples_absent","args":{}}]},{"name":"Stability & Change Management","score":0,"verdict":"unverified","reasons":["Stability not yet verified: not enough scan history yet (needs a 30-day window)."],"codes":[{"code":"stability.insufficient_history","args":{}}]},{"name":"Tool Coverage","score":71,"verdict":"fail","reasons":["100% of tools have a non-trivial description (not blank, and not just the tool's name).","0% of tool parameters carry a description.","Structured output schemas are declared (100% of tools); any adoption earns full credit."],"codes":[{"code":"toolquality.descriptions","args":{"pct":"100"}},{"code":"toolquality.param_docs","args":{"pct":"0"}},{"code":"toolquality.output_present","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 10 captured tool definition(s), and no name or description among them implies an irreversible operation.","An AI judge read all 11 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":"10"}},{"code":"toolsafety.manipulation_clean","args":{"units":"11","judged":"11"}}]},{"name":"Capabilities","score":100,"verdict":"pass","reasons":["Implements a current MCP spec version (2026-07-28)."],"codes":[{"code":"protocol.current","args":{"version":"2026-07-28"}}]}],"inconclusive":["Malware scan not yet available for this package.","Build provenance not yet verified.","Stability not yet verified: not enough scan history yet (needs a 30-day window)."],"malware":[],"components":[{"slug":"biomapper","type":"pypi","identifier":"biomapper","withdrawn":false,"score":52,"current":true,"url":"https://verifymcp.io/servers/trentleslie-biomapper/biomapper","markdownUrl":"https://verifymcp.io/servers/trentleslie-biomapper/biomapper.md"}],"facts":[{"label":"Registry","value":"pypi"},{"label":"Package","value":"biomapper"},{"label":"Version","value":"1.6.2"},{"label":"Transport","value":"stdio"}],"install":{"available":true,"bundleSha256":null},"tools":[{"name":"list_entity_types","title":null,"description":"List the Biolink entity types BioMapper accepts, with aliases and default identifier prefixes. Call this first to choose entity_type for the mapping tools.","inputs":[],"outputs":[{"name":"entity_types","type":"array","required":true,"description":null}],"hasOutputSchema":true,"hasExamples":false,"tokenEstimate":39},{"name":"list_vocabularies","title":null,"description":"List the identifier vocabularies (CURIE prefixes) BioMapper knows.","inputs":[],"outputs":[{"name":"vocabularies","type":"array","required":true,"description":null}],"hasOutputSchema":true,"hasExamples":false,"tokenEstimate":25},{"name":"list_annotators","title":null,"description":"List the annotators the BioMapper mapping pipeline can use.","inputs":[],"outputs":[{"name":"annotators","type":"array","required":true,"description":null}],"hasOutputSchema":true,"hasExamples":false,"tokenEstimate":22},{"name":"server_info","title":null,"description":"Server version, KG provenance (pending until the startup probe lands), limits, and the folders map_file may read. Makes no request to BioMapper.","inputs":[],"outputs":[{"name":"allowed_roots","type":"array","required":true,"description":null},{"name":"batch_cap","type":"integer","required":true,"description":null},{"name":"loop_limit","type":"integer","required":true,"description":null},{"name":"loop_window_s","type":"number","required":true,"description":null},{"name":"provenance","type":null,"required":true,"description":null},{"name":"server_version","type":"string","required":true,"description":null}],"hasOutputSchema":true,"hasExamples":false,"tokenEstimate":38},{"name":"map_entity","title":null,"description":"Map ONE entity name to knowledge-graph identifiers. Takes about 4-5 s. Call list_entity_types first to choose entity_type (e.g. biolink:SmallMolecule for metabolites). Optional identifiers are hints, e.g. {\"HMDB\": \"HMDB0000177\"}. For more than 5 entities use map_file instead; repeated single calls are refused after a limit.","inputs":[{"name":"annotation_mode","type":"string","required":false,"description":null},{"name":"entity_type","type":"string","required":true,"description":null},{"name":"identifiers","type":null,"required":false,"description":null},{"name":"name","type":"string","required":true,"description":null}],"outputs":[{"name":"provenance","type":null,"required":true,"description":null},{"name":"result","type":null,"required":true,"description":null}],"hasOutputSchema":true,"hasExamples":false,"tokenEstimate":117},{"name":"map_batch","title":null,"description":"Map up to 5 entities of one entity_type in a single request (about 4-5 s per entity, so up to ~25 s). More than 5 is refused: write them to a TSV/CSV and use map_file.","inputs":[{"name":"annotation_mode","type":"string","required":false,"description":null},{"name":"entities","type":"array","required":true,"description":null},{"name":"entity_type","type":"string","required":true,"description":null}],"outputs":[{"name":"provenance","type":null,"required":true,"description":null},{"name":"results","type":"array","required":true,"description":null}],"hasOutputSchema":true,"hasExamples":false,"tokenEstimate":81},{"name":"map_file","title":null,"description":"Map every row of a TSV/CSV file as a resumable BACKGROUND job and return immediately with a job_id and an ETA (about 4-5 s per unique entity). Use this for more than 5 entities. The file must be inside an allowed folder (the client's roots or BIOMAPPER_MCP_ROOTS). Writes <input>.biomapper.tsv next to the input (never overwrites) plus a provenance JSON. identifier_columns maps a column name to its vocabulary, e.g. {\"hmdb_id\": \"HMDB\"}. Re-submitting the same file and options returns the existing job; rerun=true starts over with a fresh cache. Poll job_status about once a minute.","inputs":[{"name":"annotation_mode","type":"string","required":false,"description":null},{"name":"entity_type","type":"string","required":true,"description":null},{"name":"identifier_columns","type":null,"required":false,"description":null},{"name":"key_column","type":null,"required":false,"description":null},{"name":"name_column","type":"string","required":true,"description":null},{"name":"output_path","type":null,"required":false,"description":null},{"name":"path","type":"string","required":true,"description":null},{"name":"rerun","type":"boolean","required":false,"description":null}],"outputs":[{"name":"created_utc","type":"string","required":true,"description":null},{"name":"entities_done","type":"integer","required":true,"description":null},{"name":"entities_failed","type":"integer","required":false,"description":null},{"name":"entities_total","type":"integer","required":true,"description":"Unique entities (duplicate rows are mapped once)"},{"name":"eta_s","type":null,"required":false,"description":"Best-effort estimate, not a promise"},{"name":"input_path","type":"string","required":true,"description":null},{"name":"job_id","type":"string","required":true,"description":null},{"name":"kg_build","type":"string","required":false,"description":null},{"name":"kg_verified","type":"boolean","required":false,"description":null},{"name":"output_path","type":"string","required":true,"description":null},{"name":"owner","type":null,"required":false,"description":null},{"name":"partial_path","type":"string","required":true,"description":null},{"name":"pass_index","type":"integer","required":false,"description":null},{"name":"provenance_path","type":"string","required":true,"description":null},{"name":"reason","type":null,"required":false,"description":null},{"name":"rows_total","type":"integer","required":true,"description":null},{"name":"state","type":"string","required":true,"description":null},{"name":"updated_utc","type":"string","required":true,"description":null}],"hasOutputSchema":true,"hasExamples":false,"tokenEstimate":208},{"name":"job_status","title":null,"description":"Status of one map_file job (job_id) or of all jobs in the current folders: state (queued, running, paused, stalled, expired, cancelled, complete, failed, owned_elsewhere), progress, ETA estimate, output path, and whether the KG build is verified. Makes no request to BioMapper.","inputs":[{"name":"job_id","type":null,"required":false,"description":null}],"outputs":[{"name":"jobs","type":"array","required":true,"description":null},{"name":"note","type":null,"required":false,"description":null}],"hasOutputSchema":true,"hasExamples":false,"tokenEstimate":78},{"name":"resume_job","title":null,"description":"Resume a stalled, expired, paused, or cancelled job after a fresh health check. Rows already mapped are not re-mapped.","inputs":[{"name":"job_id","type":"string","required":true,"description":null}],"outputs":[{"name":"created_utc","type":"string","required":true,"description":null},{"name":"entities_done","type":"integer","required":true,"description":null},{"name":"entities_failed","type":"integer","required":false,"description":null},{"name":"entities_total","type":"integer","required":true,"description":"Unique entities (duplicate rows are mapped once)"},{"name":"eta_s","type":null,"required":false,"description":"Best-effort estimate, not a promise"},{"name":"input_path","type":"string","required":true,"description":null},{"name":"job_id","type":"string","required":true,"description":null},{"name":"kg_build","type":"string","required":false,"description":null},{"name":"kg_verified","type":"boolean","required":false,"description":null},{"name":"output_path","type":"string","required":true,"description":null},{"name":"owner","type":null,"required":false,"description":null},{"name":"partial_path","type":"string","required":true,"description":null},{"name":"pass_index","type":"integer","required":false,"description":null},{"name":"provenance_path","type":"string","required":true,"description":null},{"name":"reason","type":null,"required":false,"description":null},{"name":"rows_total","type":"integer","required":true,"description":null},{"name":"state","type":"string","required":true,"description":null},{"name":"updated_utc","type":"string","required":true,"description":null}],"hasOutputSchema":true,"hasExamples":false,"tokenEstimate":42},{"name":"cancel_job","title":null,"description":"Cancel a job. It stops after the current chunk; the partial output and cache are kept, so resume_job can continue it later.","inputs":[{"name":"job_id","type":"string","required":true,"description":null}],"outputs":[{"name":"created_utc","type":"string","required":true,"description":null},{"name":"entities_done","type":"integer","required":true,"description":null},{"name":"entities_failed","type":"integer","required":false,"description":null},{"name":"entities_total","type":"integer","required":true,"description":"Unique entities (duplicate rows are mapped once)"},{"name":"eta_s","type":null,"required":false,"description":"Best-effort estimate, not a promise"},{"name":"input_path","type":"string","required":true,"description":null},{"name":"job_id","type":"string","required":true,"description":null},{"name":"kg_build","type":"string","required":false,"description":null},{"name":"kg_verified","type":"boolean","required":false,"description":null},{"name":"output_path","type":"string","required":true,"description":null},{"name":"owner","type":null,"required":false,"description":null},{"name":"partial_path","type":"string","required":true,"description":null},{"name":"pass_index","type":"integer","required":false,"description":null},{"name":"provenance_path","type":"string","required":true,"description":null},{"name":"reason","type":null,"required":false,"description":null},{"name":"rows_total","type":"integer","required":true,"description":null},{"name":"state","type":"string","required":true,"description":null},{"name":"updated_utc","type":"string","required":true,"description":null}],"hasOutputSchema":true,"hasExamples":false,"tokenEstimate":43}],"toolsTruncatedAtCapture":false,"diagnostics":{"capturedAt":"2026-11-05T00:45:30.000Z","track":"package","endpoint":null,"declaredUrl":null,"truncated":false,"tls":null,"dnssec":null,"auth":null,"httpsRedirect":null,"transports":[],"provenance":{"outcome":"inconclusive","label":"Inconclusive","reason":"attestation_fetch_failed","reasonLabel":"Attestation not fetched","discovery":null,"discoveryLabel":null,"sourceRepo":null,"attestationSkipped":null,"attestationSkippedLabel":null},"installScripts":[{"hook":"build_backend","tier":"allowlisted"}],"installScriptsTotal":null,"vulnerabilities":[],"vulnerabilitiesTotal":null,"dependencies":{"nodes":33,"partial":false,"deprecated":null,"stale":1,"noRepo":1}},"mismatches":[],"changelog":{"trackingSince":"2026-11-05","recent":[{"id":"chg_01a1a92b-038e-7aad-809e-412090f32b96","kind":"score.first_scored","summary":"First indexed and scored","materiality":"functional","direction":"neutral","scoreDelta":null,"occurredOn":"2026-11-05","url":"https://verifymcp.io/servers/trentleslie-biomapper/biomapper#chg-chg_01a1a92b-038e-7aad-809e-412090f32b96"}],"truncated":false,"feedUrl":"https://verifymcp.io/servers/trentleslie-biomapper/biomapper/changelog.json"},"links":{"html":"https://verifymcp.io/servers/trentleslie-biomapper/biomapper","markdown":"https://verifymcp.io/servers/trentleslie-biomapper/biomapper.md","changelogJson":"https://verifymcp.io/servers/trentleslie-biomapper/biomapper/changelog.json","changelogRss":"https://verifymcp.io/servers/trentleslie-biomapper/biomapper.xml","external":[{"label":"PyPI project","href":"https://pypi.org/project/biomapper/"},{"label":"Socket report","href":"https://socket.dev/pypi/package/biomapper"},{"label":"Repository","href":"https://github.com/Phenome-Health/biomapper"}]}}