Bioportal
NPM · @PIPEWORX/MCP-BIOPORTAL · 2 COMPONENTS
BioPortal — NCBO's biomedical ontology repository (data.bioontology.org).
Available components
Last scanned (6 hours ago)
Scores higher than 76% of npm servers
Category Health and Science
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
- No install/post-install scripts declared.Pass
- No production dependencies, so there is no dependency health to assess. View diagnostics → Pass
Provenance & Transparency97
- Source repository is publicly reachable at the declared URL. View diagnostics → Pass
- Cryptographically verified build provenance (signed, bound to pipeworx-io/mcp-bioportal). View diagnostics → Pass
- Clear OSI-approved license (MIT).Pass
- Actively maintained (last published 5 days ago).Pass
- Disclosure check failed: no security disclosure policy was found in the source repository. See how to fix → Fail
Schema Quality & AI Usability67
- AI-judged instruction clarity (excellent).Pass
- Context-footprint check failed: tool/resource definitions use about 916 tokens (~229/item across 4 items; 4 tools + 0 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 Management23
- Stability observed for 7 of 30 days with no destabilising changes; credit accrues until the full window elapses.Partial
Tool Coverage100
- 100% of tools have a non-trivial description (not blank, and not just the tool's name).Pass
- 100% of tool parameters carry a description.Pass
Tool Safety100
- No prompt-injection markers were found in the server instructions, tool names or descriptions we captured.Pass
- We read all 4 captured tool definition(s), and no name or description among them implies an irreversible operation.Pass
- An AI judge read all 5 captured unit(s) of tool text and found none that tries to manipulate the model reading it.Pass
Capabilities100
- Implements a supported MCP spec version (2025-11-25); the latest is 2026-07-28.Pass
Checks we ran (16)
- Malware scan
- Known CVEs
- Install scripts
- Dependency health
- Source repository
- Provenance
- License
- Maintenance
- Security disclosure
- Schema quality
- Stability
- Tool coverage
- Injection markers
- Destructive annotations
- Judged manipulation
- MCP protocol
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 +1
No change was recorded against any check on this day. Stability & Change Management went from 20 to 23. That category is still filling its 30-day observation window: 6 days of observed history at the previous scan, 7 at this one. The score rises as the window fills, whether or not the server changes.
- 3 Nov 26 +1
No change was recorded against any check on this day. Stability & Change Management went from 13 to 17. That category is still filling its 30-day observation window: 4 days of observed history at the previous scan, 5 at this one. The score rises as the window fills, whether or not the server changes.
- 1 Nov 26 +1
No change was recorded against any check on this day. Stability & Change Management went from 7 to 10. That category is still filling its 30-day observation window: 2 days of observed history at the previous scan, 3 at this one. The score rises as the window fills, whether or not the server changes.
- 31 Oct 26 +15
- Malware scan: unverified → pass ▲ security
- 30 Oct 26 −14
- Malware scan: pass → unverified ▼ security
- Package version: 0.2.0 → 0.2.1 functional
- 29 Oct 26 79
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 npm/@pipeworx/mcp-bioportal@0.2.1
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 | npm |
| Reason | Verified |
| Discovered via | Registry attestation endpoint |
| Source repo | pipeworx-io/mcp-bioportal |
| Certificate issuer | https://token.actions.githubusercontent.com |
| Certificate SAN | https://github.com/pipeworx-io/mcp-bioportal/.github/workflows/publish.yml@refs/heads/main |
| Rekor log index | 3601451353 |
| Predicate type | SLSA build provenance https://slsa.dev/provenance/v1 |
| Subject digest | sha512:693e5a61c4d434850e7674828bb9c11fd7f5f16dac9ac46656686a7e22335a45dde564da46aa9009a63e92dcdf488db208e9d3b6dfaa9b2106e6cc251 |
Background: How many MCP packages publish verified provenance →
Dependencies 0 packages
| Packages resolved | 0 |
|---|---|
| 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 →
bioportal_class ~186
Full record for one ontology class by its IRI — preferred label, every synonym, the curated definition, semantic types, obsolescence flag, and links to parents and children. AUTHORITATIVE for the canonical meaning of a coded concept. Pass the ontology acronym and the class IRI exactly as bioportal_search returned it.
| Name | Type | Req | Description |
|---|---|---|---|
| _apiKey | string | – | Your own BioPortal API key (free, https://bioportal.bioontology.org/accounts/new). Optional — without one the call uses a shared key that NCBO rate-limits across all of its users. |
| class_id | string | yes | Full class IRI as returned by bioportal_search, e.g. "http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C3224" |
| ontology | string | yes | Ontology acronym (e.g. "NCIT") |
No output schema declared.
No examples provided.
bioportal_mappings ~243
Cross-ontology mappings for one class — the equivalent concepts in every other BioPortal ontology, with the mapping source (SAME_URI, LOOM, CUI, REST). AUTHORITATIVE for translating a code between terminologies, e.g. an NCIT concept to its SNOMEDCT, MESH and ICD10CM equivalents. Pass the ontology acronym and class IRI.
| Name | Type | Req | Description |
|---|---|---|---|
| _apiKey | string | – | Your own BioPortal API key (free, https://bioportal.bioontology.org/accounts/new). Optional — without one the call uses a shared key that NCBO rate-limits across all of its users. |
| class_id | string | yes | Full class IRI (e.g. "http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C3224") |
| limit | number | – | Max mappings to return, 1-200 (default 50) |
| ontology | string | yes | Ontology acronym the class lives in (e.g. "NCIT") |
| to_ontology | string | – | Optional: only mappings into this ontology acronym (e.g. "SNOMEDCT") |
No output schema declared.
No examples provided.
bioportal_ontologies ~165
List the biomedical ontologies BioPortal carries — acronym, full name and type — so you can pick the right vocabulary acronym before searching or looking up a class. AUTHORITATIVE catalogue of what is available in BioPortal. Pass `filter` to narrow by acronym or name substring.
| Name | Type | Req | Description |
|---|---|---|---|
| _apiKey | string | – | Your own BioPortal API key (free, https://bioportal.bioontology.org/accounts/new). Optional — without one the call uses a shared key that NCBO rate-limits across all of its users. |
| filter | string | – | Case-insensitive substring of the acronym or name (e.g. "snomed", "cancer") |
| limit | number | – | Max ontologies to return, 1-200 (default 50) |
No output schema declared.
No examples provided.
bioportal_search ~269
Search ~1,300 biomedical ontologies for a term and get back the matching classes with their preferred label, synonyms, definition, ontology and permanent class IRI. AUTHORITATIVE for mapping free text to a coded clinical concept (NCIT, SNOMEDCT, LOINC, RXNORM, MESH, HPO, ICD10CM) — these are the curated terminologies themselves, not a description of them. Restrict with `ontologies` when you know which vocabulary you want.
| Name | Type | Req | Description |
|---|---|---|---|
| _apiKey | string | – | Your own BioPortal API key (free, https://bioportal.bioontology.org/accounts/new). Optional — without one the call uses a shared key that NCBO rate-limits across all of its users. |
| exact_match | boolean | – | Only exact label/synonym matches (default false) |
| limit | number | – | Max classes to return, 1-100 (default 25) |
| ontologies | string | – | Comma-separated ontology acronyms to restrict to (e.g. "NCIT,DOID,SNOMEDCT") |
| query | string | yes | Term to search for (e.g. "melanoma", "metformin") |
| require_definitions | boolean | – | Only return classes that carry a definition |
No output schema declared.
No examples provided.
How do I install the Bioportal MCP server?
Bioportal runs locally as an npm package, launched with npx -y @pipeworx/mcp-bioportal. Ready-made configuration for Claude, Cursor, VS Code, Codex and 5 more is on this page, copied from each client's own documentation.
npm · @pipeworx/mcp-bioportal
claude mcp add pipeworx-io-bioportal -- npx -y @pipeworx/mcp-bioportal
What is the Bioportal MCP server?
Bioportal is an MCP server listed in the public MCP registry as io.github.pipeworx-io/bioportal. BioPortal, NCBO's biomedical ontology repository (data.bioontology.org). This page covers its npm package (@pipeworx/mcp-bioportal).
Is the Bioportal MCP server safe to use?
Bioportal scores 83 out of 100 on VerifyMCP. We found no known CVEs affecting it as of 5 November 2026. It declares no install or post-install scripts. 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 Bioportal MCP server expose?
Bioportal exposes 4 tools: bioportal_search, bioportal_ontologies, bioportal_class, bioportal_mappings. Their descriptions and schemas cost roughly 863 tokens of context every time the server is loaded.
Is the Bioportal MCP server still maintained?
Bioportal 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 Bioportal MCP server under?
Bioportal declares the MIT 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 Bioportal MCP server?
VerifyMCP ran 16 checks on Bioportal, covering Malware scan, Known CVEs, Install scripts, Dependency health and 12 more. Endpoint Security and Transport & Reachability do not apply to an npm package, so they were not tested. The score does not measure everything, and the scoring documentation lists what it leaves out.