# biomedmcp

> Integrated public biomedical research with cited, bounded evidence.

- name: io.github.unibio-intelligence/biomedmcp
- version: 0.2.6
- connection class: R0 (autonomous)
- trust: 93/100
- quality: 82/100 (good)
- owner: not claimed
- descriptor: https://api.protogrid.dev/v1/servers/io.github.unibio-intelligence%2Fbiomedmcp
- tools: https://api.protogrid.dev/v1/servers/io.github.unibio-intelligence%2Fbiomedmcp/tools

**An agent can connect right now, no human step.** Remote endpoint, no authentication, reachable on the last probe.

## Connection (mcpServers)

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


## Trust

- hygiene: 95
- liveness: 100
- freshness: 100
- provenance: 80
- drivers: +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.

## Quality 82/100 (good)

### protocol: 88 (weight 25)

- pass `protocol.modern`: supports 2026-07-28 (server/discover)
- pass `protocol.stateless`: answers without a session
- pass `protocol.transport`: streamable HTTP
- warn `protocol.list_ttl`: tools/list declares ttlMs 0, so clients re-fetch it on every use

### authorization: n/a (weight 15)

- n/a `auth.prm`, `auth.as_metadata`, `auth.cimd`: no remote uses OAuth
- n/a `auth.secret_in_url`: no templated URL

### tool hygiene: 94 (weight 30)

- pass `tools.descriptions`: every tool has a description
- pass `tools.description_length`: descriptions are concise
- pass `tools.schemas`: every tool has an object input schema
- pass `tools.annotations`: 13 of 13 tools declare readOnlyHint or destructiveHint
- pass `tools.directory_hints`: every tool declares readOnlyHint, destructiveHint, idempotentHint and openWorldHint
- warn `tools.token_cost`: about 9,303 tokens to load every tool
- pass `tools.api_dump`: tools are not a one-to-one API dump
- pass `tools.hidden_text`: no hidden text in tool names, descriptions, schemas or annotations

### stability: 50 (weight 15)

- warn `stability.changes`: 25 tool changes in 30 days
- fail `stability.rug_pull`: 1 tools kept their name but changed most of their description in 30 days; review before trusting them
- pass `stability.new_links`: no tool change named a new site

### dependencies: n/a (weight 15)

- n/a `deps.known_vulns`, `deps.mcp_sdk_version`, `deps.resolvable`: deps.dev does not know biomedmcp@0.2.6

- tools: 13, about 9,303 tokens to load them all
- tool set hash: 6c3cd68724f638b8275bd4604d8baa9c
- tools last changed: 2026-11-06T06:18:32.366Z
- badge: [![protogrid quality](https://protogrid.dev/badge/io.github.unibio-intelligence/biomedmcp.svg)](https://protogrid.dev/servers/io.github.unibio-intelligence/biomedmcp)
- Checks run on what our credential-free, read-only probes observe; tools are never called and no code audit is performed.

### Tool changes

- 2026-11-06 `quota` removed
  - Inspect current research allowance and reset times; sign in for higher limits. e.g. {}; biomedmcp://guide
- 2026-11-06 `research` removed
  - Dossiers retain citations/outcomes. Inspect capabilities and get further sections for completeness. e.g. {"workflow":"target_dossier","focus":"ERBB2","species":9606}; biomedmcp://guide
- 2026-11-06 `get` removed
  - 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
- 2026-11-06 `search` removed
  - 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
- 2026-11-06 `variant_evidence` removed
  - 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
- 2026-11-06 `capabilities` removed
  - Inspect enabled sources, workflows, sections or an advanced operation's exact schema. e.g. {}; biomedmcp://guide
- 2026-11-06 `batch` removed
  - 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
- 2026-11-06 `relate` removed
  - 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
- 2026-11-06 `resolve` removed
  - 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
- 2026-11-06 `study_analysis` removed
  - 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

Full history: https://api.protogrid.dev/v1/servers/io.github.unibio-intelligence%2Fbiomedmcp/changes

## Dependencies

- pypi biomedmcp@0.2.6: unknown

Dependency graphs from deps.dev; advisories from OSV.dev, including the GitHub Advisory Database and the PyPI Advisory Database; all CC BY 4.0.

## Remotes

- https://biomedmcp.unibiointelligence.com/mcp (streamable-http, auth none, reachable true, uptime30d 1)

## Packages

- pypi biomedmcp@0.2.6
- oci ghcr.io/unibio-intelligence/biomedmcp:0.2.6

## Tools (13)

- `analyze_study`: 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`: 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`: 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`: 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`: Show remaining research allowance and reset times; signed-in accounts get higher limits. e.g. {}
- `get_record`: 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`: 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`: 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`: 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`: 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`: 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`: 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`: 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"}}