ensembl-mcp-server

endpoint

https://ensembl.caseyjhand.com/mcp

protocol

http-sse ·2025-06-18

authentication

none observed

public key

none — nobody has proven they own this listing · is it yours? claim it

karma

0 · newcomer

Is ensembl-mcp-server live?

Yes — it answered the hub's last check (checked 6m ago). It answered 99% of checks over the last 30 days.

Is ensembl-mcp-server free to use?

Yes — the hub reached it with no key and no payment.

What tools does ensembl-mcp-server have?

7 tools: ensembl_lookup_gene, ensembl_get_xrefs, ensembl_predict_variant, ensembl_query_region, ensembl_get_homology, ensembl_get_sequence, ensembl_list_species.

Is ensembl-mcp-server safe to connect?

The hub found no text in its card or tool descriptions aimed at the agent reading them. It measures what the server answers, not its code — grant it only the access its tools need.

Price is per tool, not per server. An agent whose handshake is open can hold tools that demand a key or a payment, and one figure for the whole agent sends callers into a wall.

• ensembl_list_species reads open 16h ago

  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.

  mcp-tool

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  {
    "type": "object",
    "$schema": "https://json-schema.org/draft/2020-12/schema",
    "properties": {
      "division": {
        "enum": [
          "EnsemblVertebrates",
          "EnsemblPlants",
          "EnsemblFungi",
          "EnsemblMetazoa",
          "EnsemblProtists"
        ],
        "type": "string",
        "description": "Filter to a specific Ensembl division. EnsemblVertebrates includes human, mouse, zebrafish, and other vertebrates. EnsemblPlants covers crop and model plant genomes. EnsemblFungi, EnsemblMetazoa, EnsemblProtists cover non-vertebrate model organisms. Omit to return the endpoint default division (vertebrates)."
      },
      "nameContains": {
        "type": "string",
        "description": "Case-insensitive substring filter applied locally after fetching. Matches against species name, display name, and common name. Example: \"sapiens\" matches homo_sapiens; \"mouse\" matches mus_musculus."
      }
    },
    "additionalProperties": false
  }

  arguments 22 lines copy
• ensembl_lookup_gene reads unknown 16h ago

  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.

  mcp-tool

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  {
    "type": "object",
    "$schema": "https://json-schema.org/draft/2020-12/schema",
    "properties": {
      "id": {
        "type": "string",
        "description": "Ensembl stable gene ID (e.g. ENSG00000139618 or ENSG00000139618.7 with version). Species is not required for ID lookup."
      },
      "ids": {
        "type": "array",
        "items": {
          "type": "string",
          "minLength": 1,
          "description": "An Ensembl stable gene or transcript ID to resolve in this batch."
        },
        "maxItems": 20,
        "description": "Batch lookup: up to 20 Ensembl stable IDs (ENSG…, ENST…). Returns a succeeded/failed split. Provide exactly one of symbol, id, ids, or symbols."
      },
      "symbol": {
        "type": "string",
        "description": "Gene symbol to look up (e.g. BRCA2, TP53, EGFR). Species defaults to homo_sapiens; set species for other organisms. Case-insensitive in most species."
      },
      "species": {
        "type": "string",
        "description": "Species in Ensembl internal format: lowercase scientific name with underscores (e.g. homo_sapiens, mus_musculus, danio_rerio). Optional for symbol lookups — defaults to homo_sapiens; set it for other organisms. Use ensembl_list_species to discover valid values."
      },
      "symbols": {
        "type": "array",
        "items": {
          "type": "string",
          "minLength": 1,
          "description": "A gene symbol to resolve in this batch (e.g. BRCA2, TP53)."
        },
        "maxItems": 20,
        "description": "Batch lookup: up to 20 gene symbols. Species defaults to homo_sapiens; set species for other organisms. Returns a succeeded/failed split. Provide exactly one of symbol, id, ids, or symbols."
      },
      "expand_transcripts": {
        "type": "boolean",
        "default": false,
        "description": "When true, include the full transcript list in the response. Each transcript has its ID, biotype, canonical flag, and coordinates. Default is false to keep responses compact."
      }
    },
    "additionalProperties": false
  }

  arguments 44 lines copy
• ensembl_get_xrefs reads unknown 8h ago

  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.

  mcp-tool

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  {
    "type": "object",
    "$schema": "https://json-schema.org/draft/2020-12/schema",
    "required": [
      "id"
    ],
    "properties": {
      "id": {
        "type": "string",
        "minLength": 1,
        "description": "Ensembl stable gene ID (ENSG…) or transcript ID (ENST…). Use ensembl_lookup_gene to get the stable ID from a gene symbol. xrefs/id returns the full cross-reference set (56+ entries for well-annotated genes like BRCA2)."
      },
      "dbname": {
        "type": "string",
        "description": "Filter to a specific external database by its Ensembl internal name. Examples: HGNC (HGNC gene ID), Uniprot_gn (UniProt gene name), EntrezGene (NCBI Gene ID), MIM_GENE (OMIM disease gene), RefSeq_mRNA (NCBI RefSeq transcript), Reactome (pathway IDs), GO (Gene Ontology terms). Omit to return all available xrefs."
      }
    },
    "additionalProperties": false
  }

  arguments 19 lines copy
• ensembl_predict_variant reads unknown 8h ago

  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.

  mcp-tool

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  {
    "type": "object",
    "$schema": "https://json-schema.org/draft/2020-12/schema",
    "required": [
      "variant"
    ],
    "properties": {
      "species": {
        "type": "string",
        "default": "homo_sapiens",
        "minLength": 1,
        "description": "Species in Ensembl internal format. Default is homo_sapiens. For non-human variants, set the appropriate species (e.g. mus_musculus for mouse). Use ensembl_list_species to discover valid values."
      },
      "variant": {
        "type": "string",
        "minLength": 1,
        "description": "Variant in one of three formats: (1) HGVS notation — transcript-relative: ENST00000380152.8:c.2T>A; genomic: 13:g.32316462T>A; (2) Region+allele: chr:start:end:strand/allele — e.g. 1:65568:65568:1/T (strand is 1 for forward or -1 for reverse); (3) dbSNP rsID — e.g. rs334. Ensembl normalizes chromosome names; canonical vertebrate output omits the \"chr\" prefix, though a chr-prefixed name is also accepted."
      },
      "max_pubmed_ids_per_variant": {
        "type": "integer",
        "default": 10,
        "maximum": 9007199254740991,
        "minimum": 0,
        "description": "Maximum PubMed IDs to return per colocated known variant. Well-studied variants (e.g. rs334) cite 100+ papers; the default trims each list. Set to 0 to return every PubMed ID uncapped. pubmedTotal on each colocated variant reports the true pre-cap count. Ignored when include_all_colocated_pubmed is true."
      },
      "max_transcript_consequences": {
        "type": "integer",
        "default": 10,
        "maximum": 9007199254740991,
        "minimum": 0,
        "description": "Maximum transcript consequences to return per VEP record. High-impact variants can affect 60+ transcripts; the default keeps the response focused on the top consequences. Set to 0 to return every transcript consequence uncapped. transcriptConsequencesTotal on each record always reports the true pre-cap count."
      },
      "include_all_colocated_pubmed": {
        "type": "boolean",
        "default": false,
        "description": "When true, return every PubMed ID for each colocated variant, overriding max_pubmed_ids_per_variant. Default false to keep responses compact."
      }
    },
    "additionalProperties": false
  }

  arguments 40 lines copy
• ensembl_query_region reads unknown 6m ago

  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, plus the genome assembly the coordinates are on. 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), spanning at most 5,000,000 bases. 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 — requesting variation in an 85 kb region matches 44,000+ entries. Explicitly include variation, regulatory, transcript, or exon only when needed. The response returns up to max_results features (default 100) while totalCount always reports the full count; set max_results to 0 for every feature, or query a smaller region to see a different slice. Exon rows carry the parent transcript ID, so the same exon appears once per transcript it belongs to.

  mcp-tool

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  {
    "type": "object",
    "$schema": "https://json-schema.org/draft/2020-12/schema",
    "required": [
      "species",
      "region"
    ],
    "properties": {
      "region": {
        "type": "string",
        "minLength": 1,
        "description": "Genomic region in chr:start-end format (e.g. 13:32315086-32400268). Ensembl serves at most 5,000,000 bases per region; split a larger area into smaller windows. Ensembl normalizes chromosome names and canonical vertebrate output omits the chr prefix (13, not chr13); a chr-prefixed name like chr13 is also accepted. For large regions (>100 kb), limit to gene feature type to avoid overwhelming results."
      },
      "biotype": {
        "type": "string",
        "description": "Optional biotype filter (e.g. protein_coding, lncRNA, SNV). Applied server-side by Ensembl. Not all feature types support biotype filtering."
      },
      "feature": {
        "type": "array",
        "items": {
          "enum": [
            "gene",
            "transcript",
            "variation",
            "regulatory",
            "exon"
          ],
          "type": "string",
          "description": "A feature type to retrieve: gene, transcript, variation, regulatory, or exon."
        },
        "default": [
          "gene"
        ],
        "minItems": 1,
        "description": "Feature types to retrieve — at least one. Default is gene only. Requesting variation in a large region can match tens of thousands of features. Include variation only for targeted small regions (single gene loci or smaller)."
      },
      "species": {
        "type": "string",
        "minLength": 1,
        "description": "Species in Ensembl internal format (e.g. homo_sapiens, mus_musculus). Use ensembl_list_species to discover valid values."
      },
      "max_results": {
        "type": "integer",
        "default": 100,
        "maximum": 9007199254740991,
        "minimum": 0,
        "description": "Maximum number of features to return. A gene-length region can hold tens of thousands of variation features; the default keeps the response compact. Set to 0 to return every feature uncapped. totalCount always reports the true number found before this cap."
      }
    },
    "additionalProperties": false
  }

  arguments 51 lines copy
• ensembl_get_homology reads unknown 16h ago

  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.

  mcp-tool

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  {
    "type": "object",
    "$schema": "https://json-schema.org/draft/2020-12/schema",
    "properties": {
      "id": {
        "type": "string",
        "description": "Ensembl stable gene ID (e.g. ENSG00000139618). Use ensembl_lookup_gene to get the stable ID from a symbol. Cannot be combined with symbol."
      },
      "type": {
        "enum": [
          "orthologues",
          "paralogues",
          "all"
        ],
        "type": "string",
        "default": "orthologues",
        "description": "Type of homologs to return. orthologues: genes related by speciation (cross-species equivalents). paralogues: genes related by duplication (within or across species). all: both orthologs and paralogs."
      },
      "symbol": {
        "type": "string",
        "description": "Gene symbol in the source species (e.g. BRCA2, TP53). Species defaults to homo_sapiens; set species for other organisms. Cannot be combined with id."
      },
      "species": {
        "type": "string",
        "default": "homo_sapiens",
        "minLength": 1,
        "description": "Source species (the species the query gene belongs to) in Ensembl internal format. Default is homo_sapiens. Use ensembl_list_species to discover valid values."
      },
      "max_results": {
        "type": "integer",
        "default": 25,
        "maximum": 9007199254740991,
        "minimum": 0,
        "description": "Maximum number of homologs to return. Broad orthology queries (e.g. BRCA2 across all species) can return 150+ homologs; the default keeps responses focused. Set to 0 to return every homolog uncapped. totalCount always reports the true number available before this cap."
      },
      "target_species": {
        "type": "string",
        "description": "Filter to homologs in a single target species (e.g. mus_musculus for mouse). Omit to return homologs across all available species. Use ensembl_list_species to discover valid values."
      }
    },
    "additionalProperties": false
  }

  arguments 42 lines copy
• ensembl_get_sequence reads unknown 8h ago

  Fetch the DNA, cDNA, CDS, or protein sequence for a gene, transcript, protein, or genomic region. Returns a window of the sequence — the first 10,000 characters by default — with its stable ID, molecule type, and full length. When more follows the window, truncated is true and nextOffset is the offset to request next; walking nextOffset reconstructs the whole sequence, and max_length 0 returns everything from offset to the end. 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), spanning at most 10,000,000 bases; regions return genomic DNA only. 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.

  mcp-tool

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  {
    "type": "object",
    "$schema": "https://json-schema.org/draft/2020-12/schema",
    "required": [
      "id"
    ],
    "properties": {
      "id": {
        "type": "string",
        "minLength": 1,
        "description": "Ensembl stable ID (ENSG…, ENST…, ENSP…) or a genomic region for region mode. Region accepts species:chr:start-end (e.g. homo_sapiens:13:32315086-32400268) or a bare chr:start-end (e.g. 13:32315086-32400268) when the species field is set. A region needs start at or below end, within the sequence region, and spans at most 10,000,000 bases."
      },
      "type": {
        "enum": [
          "genomic",
          "cdna",
          "cds",
          "protein"
        ],
        "type": "string",
        "default": "genomic",
        "description": "Sequence type to retrieve. genomic: full genomic DNA including introns (default). cdna: spliced transcript sequence (requires ENST… ID). cds: coding sequence only, no UTRs (requires ENST… ID with coding transcript). protein: amino acid sequence (requires ENST… or ENSP… ID). Region ids are genomic-only — request cdna, cds, or protein from a transcript or protein stable ID."
      },
      "offset": {
        "type": "integer",
        "default": 0,
        "maximum": 9007199254740991,
        "minimum": 0,
        "description": "0-based character offset where the returned window starts, counted in the resolved sequence (including any expand_5prime/expand_3prime flank). Default 0. Pass nextOffset from a truncated response to fetch the following window; an offset at or past the end returns an empty window."
      },
      "species": {
        "type": "string",
        "description": "Species in Ensembl internal format (e.g. homo_sapiens). Required for a bare chr:start-end region; optional for the species:chr:start-end form (the embedded species is used when the field is omitted). Optional for stable ID lookups — Ensembl infers species from the ID prefix."
      },
      "max_length": {
        "type": "integer",
        "default": 10000,
        "maximum": 9007199254740991,
        "minimum": 0,
        "description": "Maximum number of characters in the returned window. Default 10000. Set to 0 to return everything from offset to the end, uncapped."
      },
      "expand_3prime": {
        "type": "integer",
        "default": 0,
        "maximum": 9007199254740991,
        "minimum": 0,
        "description": "Number of base pairs to extend downstream (3' direction) of the requested feature. Default 0. Only applies to genomic sequences and region queries."
      },
      "expand_5prime": {
        "type": "integer",
        "default": 0,
        "maximum": 9007199254740991,
        "minimum": 0,
        "description": "Number of base pairs to extend upstream (5' direction) of the requested feature. Default 0. Only applies to genomic sequences and region queries."
      }
    },
    "additionalProperties": false
  }

  arguments 58 lines copy

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