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8 clients · secrets stay placeholders

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{
  "mcpServers": {
    "biomedmcp": {
      "type": "http",
      "url": "https://biomedmcp.unibiointelligence.com/mcp"
    }
  }
}

claude mcp add --transport http biomedmcp https://biomedmcp.unibiointelligence.com/mcp

[mcp_servers.biomedmcp]
url = "https://biomedmcp.unibiointelligence.com/mcp"

{
  "$schema": "https://opencode.ai/config.json",
  "mcp": {
    "biomedmcp": {
      "type": "remote",
      "url": "https://biomedmcp.unibiointelligence.com/mcp",
      "enabled": true
    }
  }
}

{
  "mcpServers": {
    "biomedmcp": {
      "type": "http",
      "url": "https://biomedmcp.unibiointelligence.com/mcp"
    }
  },
  "deeplink": "cursor://anysphere.cursor-deeplink/mcp/install?name=biomedmcp&config=eyJ0eXBlIjoiaHR0cCIsInVybCI6Imh0dHBzOi8vYmlvbWVkbWNwLnVuaWJpb2ludGVsbGlnZW5jZS5jb20vbWNwIn0%3D"
}

{
  "servers": {
    "biomedmcp": {
      "type": "http",
      "url": "https://biomedmcp.unibiointelligence.com/mcp"
    }
  }
}

{
  "mcpServers": {
    "biomedmcp": {
      "httpUrl": "https://biomedmcp.unibiointelligence.com/mcp"
    }
  }
}

extensions:
  "biomedmcp":
    enabled: true
    name: "biomedmcp"
    type: streamable_http
    uri: "https://biomedmcp.unibiointelligence.com/mcp"
    timeout: 300

Quality 82 / 100good

protocol88 · weight 25

pass
protocol.modernsupports 2026-07-28 (server/discover)
pass
protocol.statelessanswers without a session
pass
protocol.transportstreamable HTTP
warn
protocol.list_ttltools/list declares ttlMs 0, so clients re-fetch it on every use

authorizationn/a · weight 15

n/a
auth.prm, auth.as_metadata, auth.cimdno remote uses OAuth
n/a
auth.secret_in_urlno templated URL

tool hygiene94 · weight 30

pass
tools.descriptionsevery tool has a description
pass
tools.description_lengthdescriptions are concise
pass
tools.schemasevery tool has an object input schema
pass
tools.annotations13 of 13 tools declare readOnlyHint or destructiveHint
pass
tools.directory_hintsevery tool declares readOnlyHint, destructiveHint, idempotentHint and openWorldHint
warn
tools.token_costabout 9,303 tokens to load every tool
pass
tools.api_dumptools are not a one-to-one API dump
pass
tools.hidden_textno hidden text in tool names, descriptions, schemas or annotations

stability50 · weight 15

warn
stability.changes25 tool changes in 30 days
fail
stability.rug_pull1 tools kept their name but changed most of their description in 30 days; review before trusting them
pass
stability.new_linksno tool change named a new site

dependenciesn/a · weight 15

n/a
deps.known_vulns, deps.mcp_sdk_version, deps.resolvabledeps.dev does not know [email protected]

13 tools, about 9,303 tokens to load them all · tool set 6c3cd68724f6 · tools last changed 2026-11-06 · checked 2026-11-14 07:03 UTC

Tool changes

2026-11-06quotaremoved
Inspect current research allowance and reset times; sign in for higher limits. e.g. {}; biomedmcp://guide
2026-11-06researchremoved
Dossiers retain citations/outcomes. Inspect capabilities and get further sections for completeness. e.g. {"workflow":"target_dossier","focus":"ERBB2","species":9606}; biomedmcp://guide
2026-11-06getremoved
Read ordinary records/evidence sections; variants use variant_evidence. Sources constrain all lookups and identity dependencies. e.g. {"entity":"gene","id":"BRAF","species":9606}; biomedmcp://guide
2026-11-06searchremoved
Find ordinary records with entity filters. Papers use literature_search; trials use trial_search. e.g. {"entity":"gene","query":"BRCA1","filters":{"species":9606}}; biomedmcp://guide
2026-11-06variant_evidenceremoved
Retrieve variant evidence with assembly/transcript ambiguity preserved. Defaults: ClinVar, population, CIViC. Request predictions for AlphaMissense, or eve for MIT-licensed EVE protein scores; computational predictions retain source and uncertainty. e.g. {"id":"BRAF V600E"}; biomedmcp://guide
2026-11-06capabilitiesremoved
Inspect enabled sources, workflows, sections or an advanced operation's exact schema. e.g. {}; biomedmcp://guide
2026-11-06batchremoved
Execute up to ten independent read operations with one atomic quota reservation. e.g. {"calls":[{"operation":"get","arguments":{"entity":"gene","id":"BRAF","species":9606}}]}; biomedmcp://guide
2026-11-06relateremoved
Traverse an evidence relationship. Relations: gene/drug/disease: articles,trials; variant: articles,structure; article: citations,references,recommendations,authors,entities; author: articles. e.g. {"entity":"article","id":"PMID:123","relation":"references"}; biomedmcp://guide
2026-11-06resolveremoved
Resolve aliases/ambiguity before evidence joins. One exact species-qualified symbol/ID resolves; provider score alone never establishes identity. Retrieve known unambiguous identifiers directly. e.g. {"entity":"gene","query":"HER2","species":9606}; biomedmcp://guide
2026-11-06study_analysisremoved
Analyze an installed verified public study. Bundled ubi_synthetic is an invented demo; discover installed releases with capabilities(source=study). Report clinical and assayed samples separately, unique mutant samples, events and exclusions. Preserve input hashes and denominators. Private compute uses Ubi platform. e.g. {"analysis":"gene_profile","study":"ubi_synthetic","gene":"TP53"}; biomedmcp://guide

Showing the latest 10. Full history: list_changes · trend: quality JSON.

Checks run on what our credential-free, read-only probes observe; tools are never called and no code audit is performed. How it is computed.

Trust 93 / 100

provenance80

liveness100

freshness100

hygiene95

+repository +namespace-matches-repo +reachable +uptime-100% +updated-5d-ago -unpinned-packages(1)

Derived from observable signals (official registry feed and our own credential-free probes); no code audit performed. How it is computed.

Dependencies

[email protected] PyPIthis version is not known to the dependency resolver

Dependency graphs from deps.dev; advisories from OSV.dev, including the GitHub Advisory Database and the PyPI Advisory Database; all CC BY 4.0. The graph is what a clean install of this version resolves today; nothing was installed or run. How it is checked.

Endpoints

remote	auth	reachable	uptime 30d	p50	protocol	last ok
`https://biomedmcp.unibiointelligence.com/mcp` streamable-http	none	yes	100%	216 ms	2026-07-28	2026-11-14

package	registry	version	runtime	secrets
`biomedmcp`	pypi	0.2.6	uvx
`ghcr.io/unibio-intelligence/biomedmcp:0.2.6`	oci	unpinned	–

Tools (13)

`analyze_study`read-only	Analyze an installed public cancer genomics study: gene_profile, mutation_cohort, survival, compare, co_occurrence, filter_cohort, top_mutated. List installed studies with get_capabilities(source=study); ubi_synthetic is invented demo data. Report sample denominators and exclusions. Private data analysis uses the Ubi platform. e.g. {"analysis":"gene_profile","study":"ubi_synthetic","gene":"TP53"}
`build_dossier`read-only	Build a multi-section dossier in one call: verified identity, default record sections and top related papers, with citations and per-source outcomes. Workflows: target_dossier, model_input_bundle (gene), drug_review, disease_landscape, pathway_review, variant_dossier, negative_evidence (bounded literature check; never proves absence). Add sections with get_record. e.g. {"workflow":"target_dossier","focus":"LDLR","species":9606}
`find_related`read-only	List records linked to one record. gene/drug/disease: articles, trials. variant: articles, structure. article: citations, references, recommendations, authors, entities. author: articles. Record attributes are get_record sections, not relations. e.g. {"entity":"article","id":"PMID:123","relation":"references"}
`get_capabilities`read-only	List enabled sources, entity sections, dossier workflows and source operations with exact parameter schemas. Narrow with source or entity; diagnose=true probes source health. Examples: biomedmcp://guide. e.g. {}
`get_quota`read-only	Show remaining research allowance and reset times; signed-in accounts get higher limits. e.g. {}
`get_record`read-only	Fetch one record by ID with optional evidence sections, e.g. gene expression/eqtl/diseases/druggability, drug label/safety, article fulltext, trial eligibility, protein domains/structures. Variants: get_variant_evidence. List an entity's sections with get_capabilities(entity=...). e.g. {"entity":"gene","id":"PCSK9","species":9606}
`get_variant_evidence`read-only	Get evidence for one variant (rsID, gene + protein change, HGVS or chr:pos:ref:alt). Defaults: ClinVar, gnomAD population, CIViC; add predictions (AlphaMissense), eve, cosmic, oncokb, hotspots, gwas or cbioportal. Ambiguous assembly or transcript is reported, not guessed; predictions keep source and uncertainty. e.g. {"id":"PCSK9 R46L"}
`query_source`read-only	Run a source-specific operation that other tools do not cover, e.g. ChEMBL bioactivities, Ensembl coordinates, PDB structure quality, OmniPath interactions, NCBI Datasets genomes, ncbi-records for GenBank/GEO/SRA. Read get_capabilities(source=...) for operations and params first. e.g. {"source":"gtex","operation":"get_metadata","params":{"info_type":"tissues","dataset_id":"gtex_v10"}}
`resolve_entity`read-only	Map a name, alias or ambiguous identifier to exact species-qualified IDs before joining evidence. Returns candidates when ambiguous; a provider match score alone is not identity. Skip when you already hold an exact ID. e.g. {"entity":"gene","query":"LDL receptor","species":9606}
`run_batch`read-only	Run up to ten independent read calls in parallel with one quota reservation; each result keeps its own outcome. build_dossier and utilities are not batchable. e.g. {"calls":[{"operation":"get_record","arguments":{"entity":"gene","id":"PCSK9","species":9606}}]}
`search_literature`read-only	Search papers across PubMed, Europe PMC, PubTator and LitSense with date, author, journal, article-type and open-access filters. Deduplicates across sources and reports each source's outcome. Read abstracts or full text with get_record(entity=article). e.g. {"query":"PCSK9 LDL cholesterol"}
`search_records`read-only	Search genes, proteins, drugs, diseases, phenotypes, pathways, variants, pharmacogenomics, GWAS, diagnostics, adverse events, studies, patents or authors by text; returns IDs for get_record (variants: get_variant_evidence). Papers: search_literature. Trials: search_trials. Patent search is chemistry-linked (SureChEMBL); assignee/inventor/CPC search is query_source(source=patents). e.g. {"entity":"gene","query":"BRCA1","filters":{"species":9606}}
`search_trials`read-only	Search clinical trials (ClinicalTrials.gov, NCI) by condition, intervention, phase and recruitment status. Read arms, eligibility or outcomes with get_record(entity=trial). Does not assess an individual's eligibility. e.g. {"query":"familial hypercholesterolemia","filters":{"status":"RECRUITING"}}

Schemas: list_tools.

Similar MCP servers

More from io.github.unibio-intelligence

Official server.json

{
  "name": "io.github.unibio-intelligence/biomedmcp",
  "title": "biomedmcp",
  "$schema": "https://static.modelcontextprotocol.io/schemas/2025-12-11/server.schema.json",
  "remotes": [
    {
      "url": "https://biomedmcp.unibiointelligence.com/mcp",
      "type": "streamable-http"
    }
  ],
  "version": "0.2.6",
  "packages": [
    {
      "version": "0.2.6",
      "transport": {
        "type": "stdio"
      },
      "identifier": "biomedmcp",
      "runtimeHint": "uvx",
      "registryType": "pypi",
      "packageArguments": [
        {
          "type": "positional",
          "value": "mcp"
        },
        {
          "name": "--transport",
          "type": "named",
          "value": "stdio"
        }
      ],
      "environmentVariables": [
        {
          "name": "UBI_PROFILE",
          "value": "local"
        }
      ]
    },
    {
      "transport": {
        "type": "stdio"
      },
      "identifier": "ghcr.io/unibio-intelligence/biomedmcp:0.2.6",
      "registryType": "oci",
      "packageArguments": [
        {
          "type": "positional",
          "value": "biomedmcp-server"
        },
        {
          "name": "--transport",
          "type": "named",
          "value": "stdio"
        }
      ],
      "environmentVariables": [
        {
          "name": "UBI_PROFILE",
          "value": "local"
        }
      ]
    }
  ],
  "repository": {
    "url": "https://github.com/unibio-intelligence/biomedmcp",
    "source": "github"
  },
  "description": "Integrated public biomedical research with cited, bounded evidence."
}