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ensembl API for agents (unofficial) — JSON over curl | clify

Ensembl (ensembl.org) genome browser: search thousands of genome assemblies, read genome metadata and stats, look up genes, transcripts, proteins, homologues, external references and variants (with predicted consequences), and fetch reference sequence through Ensembl's public JSON and GraphQL APIs.

Host: ensembl.org. Call these verified read commands with plain curl; no install, key, or account. Use the public JSON API with plain curl. No install, key, account, or browser is needed. Example: curl 'https://clify-dev.netlify.app/sites.json'. Start with /search?q=weather, then call /abc/COMMAND. Responses are one JSON object. The hosted MCP and GitHub repo are also available.

Commands

search-genomes

Search genome assemblies by name. Can list every assembly of one species by taxonomy id, and can sort (e.g. by contig N50) and paginate. Params: query, species_taxonomy_id, sort, order, page, per_page

curl 'https://clify-dev.netlify.app/ensembl/search-genomes?query=mouse&species_taxonomy_id=9606&sort=contig_n50&page=1&per_page=20'

export-genomes-csv

Download genome search results as CSV text, matching search-genomes for the same query. Params: query*, species_taxonomy_id

curl 'https://clify-dev.netlify.app/ensembl/export-genomes-csv?query=mouse&species_taxonomy_id=9606'

get-genome

Get metadata for one genome by its UUID: assembly, providers, annotation version/date, release and reference status. Params: genome_id*

curl 'https://clify-dev.netlify.app/ensembl/get-genome'

get-genome-stats

Get statistics for a genome: assembly (N50, length, GC%), coding, non-coding, pseudogene and variation counts. Params: genome_id*

curl 'https://clify-dev.netlify.app/ensembl/get-genome-stats'

get-genome-example-objects

Get example gene, location and variant ids for a genome. These are handy starting points for gene and variant lookups. Params: genome_id*

curl 'https://clify-dev.netlify.app/ensembl/get-genome-example-objects'

List popular species with their taxonomy id and number of available genomes. Params: none

curl 'https://clify-dev.netlify.app/ensembl/list-popular-species'

list-genome-groups

List genome group categories, such as external projects like VGP and BGE, with genome counts. Params: none

curl 'https://clify-dev.netlify.app/ensembl/list-genome-groups'

get-genome-counts

Get the total number of genomes in Ensembl and the count per taxonomic group (Animals, Archaea, …). Params: none

curl 'https://clify-dev.netlify.app/ensembl/get-genome-counts'

list-releases

List Ensembl data releases (name, type integrated/partial, is_current). Params: current_only

curl 'https://clify-dev.netlify.app/ensembl/list-releases?current_only=true'

search-genes

Search genes by symbol, name or stable id within one genome. Returns stable ids, biotype and location. Params: query*, genome_id, page, per_page

curl 'https://clify-dev.netlify.app/ensembl/search-genes'

search-variants

Search variants (e.g. by rsID) within one genome. Params: query*, genome_id, page, per_page

curl 'https://clify-dev.netlify.app/ensembl/search-variants'

get-gene-summary

Get a gene's versioned stable id, symbol, chromosome location, strand and biotype. Params: geneId*, genomeId

curl 'https://clify-dev.netlify.app/ensembl/get-gene-summary'

get-gene-overview

Get a gene's full name, alternative symbols (synonyms), HGNC accession and biotype. Params: geneId*, genomeId

curl 'https://clify-dev.netlify.app/ensembl/get-gene-overview'

get-gene-structure

Get a gene's transcripts with exon layout, CDS coordinates, protein product ids and canonical/MANE flags. This is what the feature explorer gene view draws. Params: geneId*, genomeId

curl 'https://clify-dev.netlify.app/ensembl/get-gene-structure'

list-gene-transcripts

List all transcripts of a gene with biotype, length, canonical/MANE status and protein length. Also returns the gene location and region checksum. Params: geneId*, genomeId

curl 'https://clify-dev.netlify.app/ensembl/list-gene-transcripts'

get-gene-external-references

Get cross-references (NCBI Gene, HGNC, OMIM, GeneCards, UniProt, RefSeq, …) for a gene and for each of its transcripts and proteins. Params: geneId*, genomeId

curl 'https://clify-dev.netlify.app/ensembl/get-gene-external-references'

get-gene-homologies

List homologues/orthologues of a gene in other species, with homology type and percent identity/coverage. Params: geneId*, genomeId

curl 'https://clify-dev.netlify.app/ensembl/get-gene-homologies'

get-transcript

Get one transcript's location, exons, CDS coordinates and protein product (id, length, sequence checksum). Params: transcriptId*, genomeId

curl 'https://clify-dev.netlify.app/ensembl/get-transcript'

get-protein-domains

Get a protein's length and its domain/family matches (Pfam, PANTHER, InterPro, …) with positions. Params: productId*, genomeId

curl 'https://clify-dev.netlify.app/ensembl/get-protein-domains'

get-protein-structure-stats

Get PDBe summary counts for a UniProt accession: number of PDB structures, ligands, interaction partners and similar proteins. Params: uniprot_id*

curl 'https://clify-dev.netlify.app/ensembl/get-protein-structure-stats'

get-variant

Get variant details: location, alleles, allele type, dbSNP source, VEP prediction, citation count, phenotype assertions and population allele frequencies. Params: variantId*, genomeId

curl 'https://clify-dev.netlify.app/ensembl/get-variant'

get-variant-consequences

Get the predicted molecular consequences of each allele of a variant on overlapping transcripts: consequence terms plus cDNA, CDS and protein positions with ref/alt. Params: variantId*, genomeId

curl 'https://clify-dev.netlify.app/ensembl/get-variant-consequences'

get-region

Get a chromosome/region's length, topology and sequence checksum. Use the checksum with get-sequence. Params: regionName*, genomeId

curl 'https://clify-dev.netlify.app/ensembl/get-region'

get-sequence

Fetch raw DNA or protein sequence (plain text) for a sequence checksum over a coordinate range, via refget. Uses 0-based start and exclusive end. Params: checksum*, start, end

curl 'https://clify-dev.netlify.app/ensembl/get-sequence?start=230710027&end=230710068'