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mcp server

ensembl-mcp-server

Look up genes, fetch sequences, predict variant consequences, find orthologs and xrefs via Ensembl.

Description as published by the maintainer. Source

  • version 0.4.2
  • active

active — Most recent push to the repository was 2026-07-09.

What this server can do

7 functions, named and described by the server itself. Parameter names are shown because they say more about what a function does than its name usually does.

ensembl_get_homology(id, type, symbol, species, max_results, target_species)
Find orthologs and/or paralogs of a gene across species. Returns each homolog's stable ID, species, homology type (ortholog_one2one, ortholog_one2many, paralog_many2many, etc.), perc_id (percent identity), perc_pos (percent positives), and taxonomy level. Essential for cross-species research — for example, "what is the mouse equivalent of human TP53?" or "how conserved is BRCA2 across mammals?". Provide either symbol + species or a stable gene ID. Target species can be filtered to a single species or left open to return all available homologs.
ensembl_get_sequence(id, type, species, expand_3prime, expand_5prime)
Fetch the DNA, cDNA, CDS, or protein sequence for a gene, transcript, protein, or genomic region. Returns the sequence with its stable ID, molecule type, and character count — large sequences are returned in full but the length is stated so callers can budget context. The type parameter selects which sequence is fetched: genomic (default, includes introns), cdna (spliced transcript), cds (coding sequence only), protein. For region mode, set id to a region — either species:chr:start-end (e.g. homo_sapiens:13:32315086-32400268) or a bare chr:start-end with species set (e.g. id 13:32315086-32400268, species homo_sapiens). Protein sequences require a transcript or protein stable ID (ENST…/ENSP…), not a gene ID — use ensembl_lookup_gene with expand_transcripts=true to get the canonical transcript ID first. Required: id.
ensembl_get_xrefs(id, dbname)
Retrieve cross-database references for a gene or feature — HGNC, UniProt, EntrezGene, OMIM, RefSeq, Reactome, and others. Returns each xref with its database name, primary ID, display ID, and description. The dbname filter narrows to specific databases; omit to return all xrefs. IDs returned here chain to protein (pubchem via UniProt), literature (pubmed via PubMed IDs), disease (OMIM via MIM_GENE), and pathway (Reactome) resources. Requires an Ensembl stable ID — use ensembl_lookup_gene to get the ENSG… ID first. Common dbname values: HGNC, Uniprot_gn, EntrezGene, MIM_GENE, RefSeq_mRNA, RefSeq_peptide, Reactome, GO (Gene Ontology), ChEMBL. Required: id.
ensembl_list_species(division, nameContains)
List species supported by Ensembl with display name, common name, assembly, taxon ID, and division. Required discovery step — species names like homo_sapiens are opaque to non-biologists and are the input format every other Ensembl tool expects. Filter by division to select one; use nameContains to find a species by partial name match. With no division, returns the endpoint default division — the vertebrates (~356 species on the default GRCh38 endpoint); pass a division to list that division.
ensembl_lookup_gene(id, ids, symbol, species, symbols, expand_transcripts)
Resolve a gene by symbol + species (or by stable ID) to its Ensembl ID, genomic location (chr:start-end:strand), biotype, description, and transcript list. Entry point for most workflows — the stable ID and coordinates returned here are inputs to other tools. Accepts both symbol lookup (BRCA2 + homo_sapiens) and direct ID lookup (ENSG00000139618). Supports batch lookup of up to 20 IDs or symbols in one call via the ids or symbols field. Provide exactly one of symbol, id, ids, or symbols. For symbol lookups species defaults to homo_sapiens (override for other organisms); for ID lookups species is not needed. Use ensembl_list_species to discover valid species names.
ensembl_predict_variant(species, variant, max_pubmed_ids_per_variant, max_transcript_consequences, include_all_colocated_pubmed)
Predict the functional consequences of a sequence variant using the Ensembl Variant Effect Predictor (VEP). Accepts three input formats: HGVS notation (transcript-relative, e.g. ENST00000380152.8:c.2T>A, or genomic, e.g. 13:g.32316462T>A); region+allele (chr:start:end:strand/allele, e.g. 1:65568:65568:1/T); and a dbSNP rsID (e.g. rs334). Returns the most severe consequence term, affected transcripts and genes, impact level (HIGH/MODERATE/LOW/MODIFIER), and any colocated known variants with clinical significance. HGVS input: provide the full notation including transcript version for best results. Region+allele input: Ensembl normalizes chromosome names and canonical vertebrate output omits the chr prefix (a chr-prefixed name is also accepted). By default the response caps transcript consequences (max_transcript_consequences) and per-variant PubMed IDs (max_pubmed_ids_per_variant) to keep large VEP results compact — well-studied variants like rs334 otherwise carry 60+ consequences and 100+ citations. Truthful totals are always reported; set a cap to 0 (or include_all_colocated_pubmed=true) to retrieve the full set. Required: variant.
ensembl_query_region(region, biotype, feature, species)
Find genomic features overlapping a chromosomal region: genes, transcripts, variants, regulatory elements, or exons. Returns each feature with its stable ID, type, location, biotype, and name. Useful for "what's in this locus?" and for seeding follow-up lookups. Region format is chr:start-end (e.g. 13:32315086-32400268 for the BRCA2 locus). Ensembl normalizes chromosome names and canonical vertebrate output omits the chr prefix (13, not chr13); a chr-prefixed name like chr13 is also accepted. The feature parameter defaults to gene only to prevent overwhelming returns — requesting variation in an 85 kb region returns 44,000+ entries. Explicitly include variation, regulatory, transcript, or exon only when needed. Exon rows carry the parent transcript ID, so the same exon appears once per transcript it belongs to. Required: species, region.

Last successful function declaration observed on . Source: https://ensembl.caseyjhand.com/mcp. We list what the server declared; we do not call any of these functions.

Endpoint status observed on . Source: https://ensembl.caseyjhand.com/mcp.

Signals

These are separate measurements of different things. They are deliberately not combined into one score, because a popularity number that mixes website traffic with saves and stars cannot be checked or acted on.

Signal Value What it measures Window Observed Source
GitHub stars 2 Number of GitHub accounts that bookmarked this repository since it was created. It is a bookmark count, not installs, not active users and not quality. cumulative, all time GitHub
Last commit 2026-07-09 Date of the most recent push to any branch. This is the strongest cheap indicator of whether the project is still maintained. point in time GitHub
Open issues 2 Open issues plus open pull requests, as GitHub counts them together. A high number can mean an active project or an abandoned one. as of fetch GitHub
Latest published version 0.4.2 Latest version string the maintainer published to the registry. as of fetch Model Context Protocol
Registry record last updated 2026-07-09 When the registry record was last updated by its maintainer. point in time Model Context Protocol
License Apache-2.0 Licence GitHub detected in the repository. Detection can be wrong; the LICENSE file is authoritative. as of fetch GitHub
First listed in the MCP Registry 2026-07-09 Date this server was first published to the official MCP Registry. Not a usage or quality measure. point in time Model Context Protocol
repository status active The repository exists on GitHub and is not archived. This says nothing about how recently it was worked on. as of fetch GitHub
mcp tools declared 7 tools Number of functions the server itself declared when asked to list them. This is what the server offers an agent, not a measure of how well any of them work. as of probe ensembl.caseyjhand.com
mcp endpoint status ok The server listed 7 functions when asked. as of probe ensembl.caseyjhand.com

Where to get it

Related, by what their authors tagged them

  • io.github.cyanheads/gnomad-genetics-mcp-server — last commit 2026-07-30, shares bioinformatics, cyanheads, genomics
    Look up allele frequencies by ancestry, gene constraint, variants, and coverage over gnomAD.
  • io.github.berntpopp/genefoundry — last commit 2026-08-01, shares bioinformatics, genomics
    MCP gateway federating 21 biomedical MCP servers behind one endpoint: gnomAD, ClinVar, HPO, VEP.
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  • io.github.cyanheads/brapi-mcp-server — last commit 2026-07-16, shares bioinformatics, cyanheads
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  • io.github.cyanheads/clinicaltrialsgov-mcp-server — last commit 2026-07-26, shares bioinformatics, cyanheads
    Search ClinicalTrials.gov — find studies, retrieve results, match patients to eligible trials.
  • io.github.cyanheads/protein-mcp-server — last commit 2026-07-30, shares bioinformatics, cyanheads
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  • io.github.cyanheads/pubchem-mcp-server — last commit 2026-07-30, shares bioinformatics, cyanheads
    Search PubChem compounds, properties, safety data, bioactivity, and cross-references.
  • io.github.cyanheads/pubmed-mcp-server — last commit 2026-07-30, shares bioinformatics, cyanheads
    Search PubMed/Europe PMC, fetch articles and full text (PMC/EPMC/Unpaywall), citations, MeSH terms.
  • io.github.cyanheads/uniprot-mcp-server — last commit 2026-07-30, shares bioinformatics, cyanheads
    Protein research over UniProtKB — search by function, fetch curated records, map IDs, proteomes.
  • ENCODE Toolkit — last commit 2026-07-26, shares bioinformatics
    20 MCP tools + 48 skills for ENCODE Project genomics — search, download, pipelines

These share tags the maintainers applied themselves, such as bioinformatics, cyanheads, genomics. Common tags like "mcp" or "ai" are ignored for this: agreeing with six hundred other projects is not a similarity.

This is not a recommendation and not a test result. It is a map of what the authors said their work is about.

Also from cyanheads

How the author describes it

Topics the maintainer set on GitHub: ai-agents, ai-tools, bioinformatics, cyanheads, ensembl, genes, genomics, mcp, mcp-server, model-context-protocol, typescript.

This record as data

Every field on this page, with its source and observation date, is in the catalog JSON. Fetch the whole kind at once instead of parsing this HTML.

GET /api/v1/entries/mcp_server.json

Sources

  1. cyanheads/ensembl-mcp-server on GitHub — GitHub, observed , trust tier 3.
  2. Tools declared by the MCP server at https://ensembl.caseyjhand.com/mcp — ensembl.caseyjhand.com, observed , trust tier 4.
  3. Official MCP Registry — Model Context Protocol, observed , trust tier 1.