Ensembl
NPM · @PIPEWORX/MCP-ENSEMBL · 2 COMPONENTS
Ensembl REST MCP.
Available components
Last scanned (12 hours ago)
Scores higher than 69% 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-ensembl). View diagnostics → Pass
- Clear OSI-approved license (MIT).Pass
- Actively maintained (last published 3 days ago).Pass
- Disclosure check failed: no security disclosure policy was found in the source repository. See how to fix → Fail
Schema Quality & AI Usability64
- AI-judged instruction clarity (good).Pass
- Context-footprint check failed: tool/resource definitions use about 1227 tokens (~175/item across 7 items; 7 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 Coverage85
- 100% of tools have a non-trivial description (not blank, and not just the tool's name).Pass
- 55% of tool parameters carry a description.Partial
Tool Safety100
- No prompt-injection markers were found in the server instructions, tool names or descriptions we captured.Pass
- We read all 7 captured tool definition(s), and no name or description among them implies an irreversible operation.Pass
- An AI judge read all 8 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.
- 4 Nov 26 +1
No change was recorded against any check on this day. Stability & Change Management went from 17 to 20. That category is still filling its 30-day observation window: 5 days of observed history at the previous scan, 6 at this one. The score rises as the window fills, whether or not the server changes.
- 2 Nov 26 +1
No change was recorded against any check on this day. Stability & Change Management went from 10 to 13. That category is still filling its 30-day observation window: 3 days of observed history at the previous scan, 4 at this one. The score rises as the window fills, whether or not the server changes.
- 1 Nov 26 0
- Stability: 0.07 → unverified ▼ security
- Tool safety: pass → unverified ▼ security
- Capabilities: pass → unverified ▼ functional
- Tool coverage: 100 → unverified ▼ functional
- First check of Schema quality: unverified functional
- Package version: 0.2.0 → 0.2.1 functional
- 31 Oct 26 +1
No change was recorded against any check on this day. Stability & Change Management went from 3 to 7. That category is still filling its 30-day observation window: 1 days of observed history at the previous scan, 2 at this one. The score rises as the window fills, whether or not the server changes.
- 29 Oct 26 78
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-ensembl@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-ensembl |
| Certificate issuer | https://token.actions.githubusercontent.com |
| Certificate SAN | https://github.com/pipeworx-io/mcp-ensembl/.github/workflows/publish.yml@refs/heads/main |
| Rekor log index | 3635921777 |
| Predicate type | SLSA build provenance https://slsa.dev/provenance/v1 |
| Subject digest | sha512:971c9e16079395d396b019372661411df12395d178f8b7dcdf10e437590f2dc0ee778b32166ef7a52cfa4a6d0bffb8ffaa8711895e1baeb754ad71b70 |
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 →
homology ~97
"What's the mouse / rat / zebrafish ortholog of [human gene]" / "ortholog of [gene] in [species]" / "homologs of [gene]" — orthologs and paralogs for a gene across species. Use for cross-species comparison, model organism work, evolutionary analysis.
| Name | Type | Req | Description |
|---|---|---|---|
| species | string | yes | – |
| symbol_or_id | string | yes | – |
| target_species | string | – | – |
No output schema declared.
No examples provided.
lookup ~194
"Ensembl gene info for [ENSG...]" / "look up [Ensembl ID]" / "fetch [ENST.../ENSE.../ENSP...]" — fetch metadata for an Ensembl stable ID (gene / transcript / exon / translation). Returns name, biotype, chromosomal position, strand, description. Pass expand=true to include child features (transcripts of a gene, exons of a transcript). Example: ENSG00000157764 (BRAF).
| Name | Type | Req | Description |
|---|---|---|---|
| assembly | string | – | Human genome build: "GRCh38" (the default) or "GRCh37" (= hg19). Coordinates you pass and coordinates you get back are both in this build. Older variant lists, spreadsheets and published tables are u… |
| expand | boolean | – | Include child features. |
| id | string | yes | e.g. "ENSG00000157764" (BRAF) |
No output schema declared.
No examples provided.
lookup_symbol ~200
"What's the Ensembl ID for [gene symbol]" / "look up [gene] in Ensembl" / "BRCA1 / TP53 / BRAF Ensembl info" / "find gene [symbol] in [species]" — look up a gene by symbol within a species (e.g. species="human" symbol="BRCA1"). Returns Ensembl gene ID, chromosomal position, biotype, description. Use to convert HGNC gene symbols to Ensembl IDs for genomics workflows.
| Name | Type | Req | Description |
|---|---|---|---|
| assembly | string | – | Human genome build: "GRCh38" (the default) or "GRCh37" (= hg19). Coordinates you pass and coordinates you get back are both in this build. Older variant lists, spreadsheets and published tables are u… |
| expand | boolean | – | – |
| species | string | yes | e.g. "human", "mus_musculus" |
| symbol | string | yes | – |
No output schema declared.
No examples provided.
sequence ~170
"DNA / cDNA / CDS / protein sequence of [gene]" / "FASTA for [Ensembl ID]" / "get sequence of [transcript]" — sequence by Ensembl stable ID. Type defaults to "genomic"; pass "cdna", "cds", or "protein" for processed forms. Use for sequence retrieval in primer design, variant analysis, or downstream sequence tools.
| Name | Type | Req | Description |
|---|---|---|---|
| assembly | string | – | Human genome build: "GRCh38" (the default) or "GRCh37" (= hg19). Coordinates you pass and coordinates you get back are both in this build. Older variant lists, spreadsheets and published tables are u… |
| id | string | yes | – |
| type | string | – | genomic (default) | cdna | cds | protein |
No output schema declared.
No examples provided.
variation ~157
"What is [rsID]" / "look up SNP [rs...]" / "variant info for [rsN]" — fetch a genetic variation record by ID (e.g. rs56116432). Returns alleles, genomic location, clinical significance, gene mappings. Use for SNP lookups, pharmacogenomics, GWAS follow-up.
| Name | Type | Req | Description |
|---|---|---|---|
| assembly | string | – | Human genome build: "GRCh38" (the default) or "GRCh37" (= hg19). Coordinates you pass and coordinates you get back are both in this build. Older variant lists, spreadsheets and published tables are u… |
| species | string | yes | – |
| variant_id | string | yes | e.g. "rs56116432" |
No output schema declared.
No examples provided.
vep ~270
"What's the effect of [variant]" / "predict consequences of [genomic change]" / "VEP for [chrom:pos]" — Variant Effect Predictor for a specified region + allele. Returns consequences (missense, synonymous, splice, etc.), affected genes, transcript impacts, SIFT/PolyPhen predictions. Use for variant interpretation in clinical or research genomics. THE REGION IS REQUIRED — there is no default. A GRCh37/hg19 position is also a valid GRCh38 position, so an unstated build cannot be detected, only guessed wrong, and a wrong guess returns confident annotations for a DIFFERENT gene rather than an error.
| Name | Type | Req | Description |
|---|---|---|---|
| allele | string | yes | e.g. "C" |
| assembly | string | yes | REQUIRED. The genome build your region is in: "GRCh38" (= hg38) or "GRCh37" (= hg19). There is no default on purpose — a genomic position is valid in BOTH builds, so an unstated build cannot be detec… |
| region | string | yes | e.g. "9:22125504-22125504:1" — in the build named by assembly. |
| species | string | yes | – |
No output schema declared.
No examples provided.
xrefs ~85
"What's the UniProt / HGNC / RefSeq ID for [gene]" / "cross-references for [gene symbol]" — external database IDs (UniProt, RefSeq, HGNC, Entrez, OMIM, etc.) for a gene symbol. Use to map between bio-database identifier spaces.
| Name | Type | Req | Description |
|---|---|---|---|
| species | string | yes | – |
| symbol | string | yes | – |
No output schema declared.
No examples provided.
How do I install the Ensembl MCP server?
Ensembl runs locally as an npm package, launched with npx -y @pipeworx/mcp-ensembl. 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-ensembl
claude mcp add pipeworx-io-ensembl -- npx -y @pipeworx/mcp-ensembl
What is the Ensembl MCP server?
Ensembl is an MCP server listed in the public MCP registry as io.github.pipeworx-io/ensembl. Ensembl REST MCP. This page covers its npm package (@pipeworx/mcp-ensembl).
Is the Ensembl MCP server safe to use?
Ensembl scores 81 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 Ensembl MCP server expose?
Ensembl exposes 7 tools: lookup, lookup_symbol, xrefs, sequence, homology, and 2 more. Their descriptions and schemas cost roughly 1,173 tokens of context every time the server is loaded.
Is the Ensembl MCP server still maintained?
Ensembl 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 Ensembl MCP server under?
Ensembl 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 Ensembl MCP server?
VerifyMCP ran 16 checks on Ensembl, 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.