{"ok":true,"site":"ensembl","host":"ensembl.org","about":"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.","commands":[{"command":"search-genomes","summary":"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":[{"name":"query","type":"string","description":"Free-text search: common name, scientific name or assembly name/accession"},{"name":"species_taxonomy_id","type":"string","description":"NCBI species taxonomy id. Restricts results to all assemblies of that species (e.g. 9606 = human, 10090 = mouse)"},{"name":"sort","type":"string","description":"Field to sort by, e.g. contig_n50. Omit for relevance ranking"},{"name":"order","type":"string","description":"Sort direction","oneOf":["asc","desc"]},{"name":"page","type":"number","description":"1-based page number","default":1},{"name":"per_page","type":"number","description":"Results per page (UI offers 20 or 100)","default":20}],"exampleUrl":"https://clify-dev.netlify.app/ensembl/search-genomes?query=mouse&species_taxonomy_id=9606&sort=contig_n50&page=1&per_page=20"},{"command":"export-genomes-csv","summary":"Download genome search results as CSV text, matching search-genomes for the same query.","params":[{"name":"query","type":"string","required":true,"description":"Free-text genome search query"},{"name":"species_taxonomy_id","type":"string","description":"NCBI species taxonomy id that restricts the export to one species' assemblies"}],"exampleUrl":"https://clify-dev.netlify.app/ensembl/export-genomes-csv?query=mouse&species_taxonomy_id=9606"},{"command":"get-genome","summary":"Get metadata for one genome by its UUID: assembly, providers, annotation version/date, release and reference status.","params":[{"name":"genome_id","type":"string","required":true,"description":"Genome UUID (genome_id from search-genomes)"}],"exampleUrl":"https://clify-dev.netlify.app/ensembl/get-genome"},{"command":"get-genome-stats","summary":"Get statistics for a genome: assembly (N50, length, GC%), coding, non-coding, pseudogene and variation counts.","params":[{"name":"genome_id","type":"string","required":true,"description":"Genome UUID"}],"exampleUrl":"https://clify-dev.netlify.app/ensembl/get-genome-stats"},{"command":"get-genome-example-objects","summary":"Get example gene, location and variant ids for a genome. These are handy starting points for gene and variant lookups.","params":[{"name":"genome_id","type":"string","required":true,"description":"Genome UUID"}],"exampleUrl":"https://clify-dev.netlify.app/ensembl/get-genome-example-objects"},{"command":"list-popular-species","summary":"List popular species with their taxonomy id and number of available genomes.","params":[],"exampleUrl":"https://clify-dev.netlify.app/ensembl/list-popular-species"},{"command":"list-genome-groups","summary":"List genome group categories, such as external projects like VGP and BGE, with genome counts.","params":[],"exampleUrl":"https://clify-dev.netlify.app/ensembl/list-genome-groups"},{"command":"get-genome-counts","summary":"Get the total number of genomes in Ensembl and the count per taxonomic group (Animals, Archaea, …).","params":[],"exampleUrl":"https://clify-dev.netlify.app/ensembl/get-genome-counts"},{"command":"list-releases","summary":"List Ensembl data releases (name, type integrated/partial, is_current).","params":[{"name":"current_only","type":"boolean","description":"Only return the current release(s)","default":true}],"exampleUrl":"https://clify-dev.netlify.app/ensembl/list-releases?current_only=true"},{"command":"search-genes","summary":"Search genes by symbol, name or stable id within one genome. Returns stable ids, biotype and location.","params":[{"name":"query","type":"string","required":true,"description":"Gene symbol, name or Ensembl stable id"},{"name":"genome_id","type":"string","description":"Genome UUID to search in (default: Human GRCh38.p14)","default":"59871324-7803-4234-856e-2a2bd96d7b3c"},{"name":"page","type":"number","description":"1-based page number","default":1},{"name":"per_page","type":"number","description":"Results per page","default":50}],"exampleUrl":"https://clify-dev.netlify.app/ensembl/search-genes"},{"command":"search-variants","summary":"Search variants (e.g. by rsID) within one genome.","params":[{"name":"query","type":"string","required":true,"description":"Variant identifier, e.g. an rsID"},{"name":"genome_id","type":"string","description":"Genome UUID (default: Human GRCh38.p14)","default":"59871324-7803-4234-856e-2a2bd96d7b3c"},{"name":"page","type":"number","description":"1-based page number","default":1},{"name":"per_page","type":"number","description":"Results per page","default":50}],"exampleUrl":"https://clify-dev.netlify.app/ensembl/search-variants"},{"command":"get-gene-summary","summary":"Get a gene's versioned stable id, symbol, chromosome location, strand and biotype.","params":[{"name":"geneId","type":"string","required":true,"description":"Ensembl gene stable id (unversioned ok), e.g. ENSG00000139618"},{"name":"genomeId","type":"string","description":"Genome UUID (default: Human GRCh38.p14)","default":"59871324-7803-4234-856e-2a2bd96d7b3c"}],"exampleUrl":"https://clify-dev.netlify.app/ensembl/get-gene-summary"},{"command":"get-gene-overview","summary":"Get a gene's full name, alternative symbols (synonyms), HGNC accession and biotype.","params":[{"name":"geneId","type":"string","required":true,"description":"Ensembl gene stable id"},{"name":"genomeId","type":"string","description":"Genome UUID (default: Human GRCh38.p14)","default":"59871324-7803-4234-856e-2a2bd96d7b3c"}],"exampleUrl":"https://clify-dev.netlify.app/ensembl/get-gene-overview"},{"command":"get-gene-structure","summary":"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":[{"name":"geneId","type":"string","required":true,"description":"Ensembl gene stable id"},{"name":"genomeId","type":"string","description":"Genome UUID (default: Human GRCh38.p14)","default":"59871324-7803-4234-856e-2a2bd96d7b3c"}],"exampleUrl":"https://clify-dev.netlify.app/ensembl/get-gene-structure"},{"command":"list-gene-transcripts","summary":"List all transcripts of a gene with biotype, length, canonical/MANE status and protein length. Also returns the gene location and region checksum.","params":[{"name":"geneId","type":"string","required":true,"description":"Ensembl gene stable id"},{"name":"genomeId","type":"string","description":"Genome UUID (default: Human GRCh38.p14)","default":"59871324-7803-4234-856e-2a2bd96d7b3c"}],"exampleUrl":"https://clify-dev.netlify.app/ensembl/list-gene-transcripts"},{"command":"get-gene-external-references","summary":"Get cross-references (NCBI Gene, HGNC, OMIM, GeneCards, UniProt, RefSeq, …) for a gene and for each of its transcripts and proteins.","params":[{"name":"geneId","type":"string","required":true,"description":"Ensembl gene stable id"},{"name":"genomeId","type":"string","description":"Genome UUID (default: Human GRCh38.p14)","default":"59871324-7803-4234-856e-2a2bd96d7b3c"}],"exampleUrl":"https://clify-dev.netlify.app/ensembl/get-gene-external-references"},{"command":"get-gene-homologies","summary":"List homologues/orthologues of a gene in other species, with homology type and percent identity/coverage.","params":[{"name":"geneId","type":"string","required":true,"description":"Versioned Ensembl gene stable id, e.g. ENSG00000139618.19 (use stable_id from get-gene-summary)"},{"name":"genomeId","type":"string","description":"Genome UUID (default: Human GRCh38.p14)","default":"59871324-7803-4234-856e-2a2bd96d7b3c"}],"exampleUrl":"https://clify-dev.netlify.app/ensembl/get-gene-homologies"},{"command":"get-transcript","summary":"Get one transcript's location, exons, CDS coordinates and protein product (id, length, sequence checksum).","params":[{"name":"transcriptId","type":"string","required":true,"description":"Versioned Ensembl transcript stable id, e.g. ENST00000366667.6"},{"name":"genomeId","type":"string","description":"Genome UUID (default: Human GRCh38.p14)","default":"59871324-7803-4234-856e-2a2bd96d7b3c"}],"exampleUrl":"https://clify-dev.netlify.app/ensembl/get-transcript"},{"command":"get-protein-domains","summary":"Get a protein's length and its domain/family matches (Pfam, PANTHER, InterPro, …) with positions.","params":[{"name":"productId","type":"string","required":true,"description":"Versioned Ensembl protein stable id, e.g. ENSP00000369497.3"},{"name":"genomeId","type":"string","description":"Genome UUID (default: Human GRCh38.p14)","default":"59871324-7803-4234-856e-2a2bd96d7b3c"}],"exampleUrl":"https://clify-dev.netlify.app/ensembl/get-protein-domains"},{"command":"get-protein-structure-stats","summary":"Get PDBe summary counts for a UniProt accession: number of PDB structures, ligands, interaction partners and similar proteins.","params":[{"name":"uniprot_id","type":"string","required":true,"description":"UniProt accession, e.g. P51587 (BRCA2)"}],"exampleUrl":"https://clify-dev.netlify.app/ensembl/get-protein-structure-stats"},{"command":"get-variant","summary":"Get variant details: location, alleles, allele type, dbSNP source, VEP prediction, citation count, phenotype assertions and population allele frequencies.","params":[{"name":"variantId","type":"string","required":true,"description":"Variant id in the form {chromosome}:{position}:{rsID}, e.g. 1:230710048:rs699"},{"name":"genomeId","type":"string","description":"Genome UUID (default: Human GRCh38.p14)","default":"59871324-7803-4234-856e-2a2bd96d7b3c"}],"exampleUrl":"https://clify-dev.netlify.app/ensembl/get-variant"},{"command":"get-variant-consequences","summary":"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":[{"name":"variantId","type":"string","required":true,"description":"Variant id {chromosome}:{position}:{rsID}"},{"name":"genomeId","type":"string","description":"Genome UUID (default: Human GRCh38.p14)","default":"59871324-7803-4234-856e-2a2bd96d7b3c"}],"exampleUrl":"https://clify-dev.netlify.app/ensembl/get-variant-consequences"},{"command":"get-region","summary":"Get a chromosome/region's length, topology and sequence checksum. Use the checksum with get-sequence.","params":[{"name":"regionName","type":"string","required":true,"description":"Region/chromosome name, e.g. 1, X, MT"},{"name":"genomeId","type":"string","description":"Genome UUID (default: Human GRCh38.p14)","default":"59871324-7803-4234-856e-2a2bd96d7b3c"}],"exampleUrl":"https://clify-dev.netlify.app/ensembl/get-region"},{"command":"get-sequence","summary":"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":[{"name":"checksum","type":"string","required":true,"description":"Sequence checksum: a region checksum from get-region, or a protein sequence checksum from get-transcript"},{"name":"start","type":"number","description":"0-based start coordinate (inclusive). For a 1-based genomic position P, use P-1. Example: 230710027 for a variant flank"},{"name":"end","type":"number","description":"End coordinate (exclusive, 0-based). Equals the 1-based inclusive end. Length returned = end - start"}],"exampleUrl":"https://clify-dev.netlify.app/ensembl/get-sequence?start=230710027&end=230710068"}]}