biomedmcp
PYPI · BIOMEDMCP · 3 COMPONENTS
Integrated public biomedical research with cited, bounded evidence.
Last scanned (11 hours ago)
Scores higher than 70% of PyPI servers
How this component scores in each security and reliability category. Every signal is checked automatically from public evidence about the published package, including repeated runs of it in an isolated sandbox, and we only credit what we can confirm. How we score → Why this is hard to score →
Supply Chain Security100
- No malware found by supply-chain analysis.Pass
- No known CVEs affecting this package version or its production dependencies.Pass
- Runs hatchling.build at install time, a recognised build step with no custom scripting around it. View diagnostics → Pass
- 4 of 73 dependencies flagged as unhealthy. View diagnostics → Partial
Provenance & Transparency97
- Source repository is publicly reachable at the declared URL. View diagnostics → Pass
- Cryptographically verified build provenance (signed, bound to unibio-intelligence/biomedmcp). View diagnostics → Pass
- Clear OSI-approved license (Apache-2.0).Pass
- Actively maintained (last published 0 days ago).Pass
- Disclosure check failed: no security disclosure policy was found in the source repository. See how to fix → Fail
Schema Quality & AI Usability38
- 0% of prompts and resources have a non-trivial description (not blank, and not just the item's name).Fail
- AI-judged instruction clarity (good).Pass
- Context-footprint check failed: tool/resource definitions use about 2131 tokens (~133/item across 16 items; 13 tools + 3 resources), over budget; trim descriptions and params. See how to fix → Fail
- Usage-examples check failed: none of the tools include examples. See how to fix → Fail
Stability & Change Management0
- Stability observed for 0 of 30 days with no destabilising changes; credit accrues until the full window elapses.Unverified
Tool Coverage90
- 100% of tools have a non-trivial description (not blank, and not just the tool's name).Pass
- 64% of tool parameters carry a description.Partial
- Structured output schemas are declared (100% of tools); any adoption earns full credit.Pass
Tool Safety100
- No prompt-injection markers were found in the server instructions, tool names or descriptions we captured.Pass
- We read all 13 captured tool definition(s), and no name or description among them implies an irreversible operation.Pass
- An AI judge read all 15 captured unit(s) of tool text and found none that tries to manipulate the model reading it.Pass
Capabilities100
- Implements a current MCP spec version (2026-07-28).Pass
Unverified: 1 category
A category scored 0 because we could not verify it: a data source with nothing on this package, evidence we could not reach, or a check we could not run. We only credit what we can confirm.
Checks we ran (15)
- Malware scan
- Known CVEs
- Install scripts
- Dependency health
- Source repository
- Provenance
- License
- Maintenance
- Security disclosure
- Schema quality
- Tool coverage
- Injection markers
- Destructive annotations
- Judged manipulation
- MCP protocol
Checks we could not complete (1)
These are gaps on our side, not findings about this package. We only credit what we can confirm, so a category made up entirely of them scores 0.
- Stability in Stability & Change Management (scores 0 for this)Stability observed for 0 of 30 days with no destabilising changes; credit accrues until the full window elapses.
Does not apply to this package (2)
- Endpoint SecurityScored on hosted endpoints only. A package has no live endpoint of its own for us to probe.
- Transport & ReachabilityScored on hosted endpoints only. A package has no live endpoint of its own for us to probe.
The score does not measure everything. What the score does not measure →
Every change we have recorded for this component, newest first. Security-relevant changes are always shown. ▲ marks a change for the better, ▼ a change for the worse; unmarked changes are neutral.
- 5 Nov 26 73
First indexed and scored.
Diagnostic detail from the automated scan of this channel: what the scanner observed at each step, so you can see exactly where a check passed or failed. It is informational only and never changes the trust score.
Captured 5 Nov 2026 · Analysed pypi/biomedmcp@0.2.4
Provenance Verified
A signed build attestation was found and verified, binding this exact artifact to the source repository it claims to come from.
| Result | Verified |
|---|---|
| Ecosystem | pypi |
| Reason | Verified |
| Discovered via | Registry attestation endpoint |
| Source repo | unibio-intelligence/biomedmcp |
| Certificate issuer | https://token.actions.githubusercontent.com |
| Certificate SAN | https://github.com/unibio-intelligence/biomedmcp/.github/workflows/registries.yml@refs/heads/main |
| Rekor log index | 3692529662 |
| Predicate type | PyPI publish attestation https://docs.pypi.org/attestations/publish/v1 |
| Subject digest | sha256:a5f76dbc48117fac2990c0d86bdaf8d4dea7cfc4f1f07e03777ca51005f26c33 |
Background: How many MCP packages publish verified provenance →
Install scripts 1 script
| Hook | Tier | Command |
|---|---|---|
| build_backend | Known build tool | hatchling.build |
Background: Why install scripts are a supply-chain risk →
Dependencies 73 packages
| Packages resolved | 73 |
|---|---|
| Stale | 3 |
| No linked repository | 1 |
| Tree resolution | Complete |
Background: SBOMs and build attestations, explained →
The tools this component advertises to a client, with an estimated token cost for each. Expand a tool to see its parameters and schema. The per-tool counts are indicative and are not scored directly; the schema's total context footprint is one signal in Schema Quality & AI Usability. A tool's description is untrusted text the model reads on every call, which is what makes this list a security surface and not just an inventory: how tool poisoning works →
analyze_study Analyze genomics study ~96
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"}
Input schema present but exposes no named parameters.
Structured output declared, but exposes no named fields.
No examples provided.
build_dossier Build research dossier ~194
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}
| Name | Type | Req | Description |
|---|---|---|---|
| assembly | – | – | Genome build for coordinate IDs. |
| focus | string | yes | Gene symbol, drug, disease (MONDO ID or name), pathway (R-HSA ID or exact name), variant, or topic. |
| section_parameters | – | – | Options keyed by requested section. |
| sections | array|null | – | Replace the workflow's default sections. |
| species | integer | – | NCBI taxon ID; 9606 is human. |
| workflow | – | yes | – |
Structured output declared, but exposes no named fields.
No examples provided.
find_related Find related records ~149
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"}
| Name | Type | Req | Description |
|---|---|---|---|
| assembly | – | – | Genome build for coordinate IDs. |
| entity | – | yes | – |
| id | string | yes | Record ID, e.g. PCSK9, PMID:123 or openalex:A123. |
| limit | integer | – | – |
| relation | string | yes | – |
| species | integer | – | NCBI taxon ID; 9606 is human. |
Structured output declared, but exposes no named fields.
No examples provided.
get_capabilities Inspect get_capabilities ~78
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. {}
| Name | Type | Req | Description |
|---|---|---|---|
| diagnose | boolean | – | Probe live source health (slower). |
| entity | – | – | – |
| source | string|null | – | – |
Structured output declared, but exposes no named fields.
No examples provided.
get_quota Check quota ~28
Show remaining research allowance and reset times; signed-in accounts get higher limits. e.g. {}
Input schema present but exposes no named parameters.
Structured output declared, but exposes no named fields.
No examples provided.
get_record Get record and evidence sections ~237
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}
| Name | Type | Req | Description |
|---|---|---|---|
| entity | – | yes | – |
| freshness | – | – | fresh bypasses the cache. |
| id | string | yes | Exact ID, e.g. PCSK9, PMID:123, NCT04368728, MONDO:0007750, Q8NBP7, R-HSA-109581 or an InChIKey. |
| section_parameters | – | – | Options keyed by requested section. |
| sections | array | – | Empty returns the base record; get_capabilities(entity=...) lists sections. |
| source_versions | object | – | Pin releases as {source: version}. |
| sources | array | – | Restrict lookups to these source IDs. |
| species | integer | – | NCBI taxon ID; 9606 is human. |
Structured output declared, but exposes no named fields.
No examples provided.
get_variant_evidence Get variant evidence ~188
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"}
| Name | Type | Req | Description |
|---|---|---|---|
| assembly | – | – | Genome build for coordinate IDs. |
| freshness | – | – | fresh bypasses the cache. |
| id | string | yes | rsID, gene + protein change (PCSK9 R46L), HGVS or chr:pos:ref:alt. |
| section_parameters | – | – | Options keyed by requested section. |
| sections | array | – | – |
| sources | array | – | Restrict lookups to these source IDs. |
Structured output declared, but exposes no named fields.
No examples provided.
query_source Query source directly ~149
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"}}
| Name | Type | Req | Description |
|---|---|---|---|
| freshness | – | – | fresh bypasses the cache. |
| operation | string | yes | Operation listed by get_capabilities(source=...). |
| params | object | – | Arguments for that operation's schema. |
| source | – | yes | – |
Structured output declared, but exposes no named fields.
No examples provided.
resolve_entity Resolve identifiers ~115
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}
| Name | Type | Req | Description |
|---|---|---|---|
| assembly | – | – | Genome build for coordinate IDs. |
| entity | – | – | – |
| query | string | yes | Name, alias, symbol or identifier. |
| species | integer | – | NCBI taxon ID; 9606 is human. |
Structured output declared, but exposes no named fields.
No examples provided.
run_batch Run batched reads ~97
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}}]}
| Name | Type | Req | Description |
|---|---|---|---|
| calls | array | yes | – |
| idempotency_key | string|null | – | Reuse when retrying so quota is charged once. |
Structured output declared, but exposes no named fields.
No examples provided.
search_literature Search literature ~138
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"}
| Name | Type | Req | Description |
|---|---|---|---|
| cursor | string|null | – | next_cursor from the previous page. |
| filters | – | – | – |
| freshness | – | – | fresh bypasses the cache. |
| limit | integer | – | – |
| output | – | – | summary trims excerpts; full keeps source fields. Omitted evidence stays recoverable. |
| query | string | yes | – |
Structured output declared, but exposes no named fields.
No examples provided.
search_records Search biomedical records ~185
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}}
| Name | Type | Req | Description |
|---|---|---|---|
| cursor | string|null | – | next_cursor from the previous page. |
| entity | – | yes | – |
| filters | – | – | – |
| freshness | – | – | fresh bypasses the cache. |
| limit | integer | – | – |
| output | – | – | summary trims excerpts; full keeps source fields. Omitted evidence stays recoverable. |
| query | string | yes | – |
Structured output declared, but exposes no named fields.
No examples provided.
search_trials Search clinical trials ~136
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"}}
| Name | Type | Req | Description |
|---|---|---|---|
| cursor | string|null | – | next_cursor from the previous page. |
| filters | – | – | – |
| freshness | – | – | fresh bypasses the cache. |
| limit | integer | – | – |
| output | – | – | summary trims excerpts; full keeps source fields. Omitted evidence stays recoverable. |
| query | string | yes | – |
Structured output declared, but exposes no named fields.
No examples provided.
How do I install the biomedmcp MCP server?
biomedmcp runs locally as a PyPI package, launched with uvx biomedmcp mcp --transport stdio. Ready-made configuration for Claude, Cursor, VS Code, Codex and 3 more is on this page, copied from each client's own documentation.
pypi · biomedmcp
claude mcp add unibio-intelligence-biomedmcp -- uvx biomedmcp mcp --transport stdio
What is the biomedmcp MCP server?
biomedmcp is an MCP server listed in the public MCP registry as io.github.unibio-intelligence/biomedmcp. Integrated public biomedical research with cited, bounded evidence. This page covers its PyPI package (biomedmcp).
Is the biomedmcp MCP server safe to use?
biomedmcp scores 73 out of 100 on VerifyMCP. We found no known CVEs affecting it as of 5 November 2026. Its build provenance is signed and verified. That is a record of what we were able to check automatically, not an endorsement. The category breakdown on this page shows every signal behind the number, including the ones we could not confirm.
What tools does the biomedmcp MCP server expose?
biomedmcp exposes 13 tools: search_records, get_record, search_literature, search_trials, get_variant_evidence, and 8 more. Their descriptions and schemas cost roughly 1,790 tokens of context every time the server is loaded.
Is the biomedmcp MCP server still maintained?
biomedmcp is still listed as active in the MCP registry. We last reached this channel on 5 November 2026. Those dates come from our own scans of the registry and the channel itself, not from anything the publisher announced.
What licence is the biomedmcp MCP server under?
biomedmcp declares the Apache-2.0 licence, which is OSI-approved. That covers the source only, and says nothing about the cost of any service it calls.
What did VerifyMCP test on the biomedmcp MCP server?
VerifyMCP ran 15 checks on biomedmcp, covering Malware scan, Known CVEs, Install scripts, Dependency health and 11 more. One item could not be completed, a gap on our side rather than a finding about biomedmcp: Stability. One category scores 0 for that reason, because we only credit what we can confirm. Endpoint Security and Transport & Reachability do not apply to a PyPI package, so they were not tested. The score does not measure everything, and the scoring documentation lists what it leaves out.