Ensembl REST API Endpoints

Archive

ResourceDescription
GET archive/id/:id Uses the given identifier to return the archived sequence
POST archive/id/:id Retrieve the archived sequence for a set of identifiers

Comparative Genomics

ResourceDescription
GET genetree/id/:id Retrieves a gene tree dump for a gene tree stable identifier
GET genetree/member/id/:id Retrieves a gene tree that contains the stable identifier
GET genetree/member/symbol/:species/:symbol Retrieves a gene tree containing the gene identified by a symbol
GET alignment/region/:species/:region Retrieves genomic alignments as separate blocks based on a region and species
GET homology/id/:id Retrieves homology information (orthologs) by Ensembl gene id
GET homology/symbol/:species/:symbol Retrieves homology information (orthologs) by symbol

Cross References

ResourceDescription
GET xrefs/symbol/:species/:symbol Looks up an external symbol and returns all Ensembl objects linked to it. This can be a display name for a gene/transcript/translation, a synonym or an externally linked reference. If a gene's transcript is linked to the supplied symbol the service will return both gene and transcript (it supports transient links).
GET xrefs/id/:id Perform lookups of Ensembl Identifiers and retrieve their external references in other databases
GET xrefs/name/:species/:name Performs a lookup based upon the primary accession or display label of an external reference and returning the information we hold about the entry

Information

ResourceDescription
GET info/analysis/:species List the names of analyses involved in generating Ensembl data.
GET info/assembly/:species List the currently available assemblies for a species.
GET info/assembly/:species/:region_name Returns information about the specified toplevel sequence region for the given species.
GET info/biotypes/:species List the functional classifications of gene models that Ensembl associates with a particular species. Useful for restricting the type of genes/transcripts retrieved by other endpoints.
GET info/compara/methods List all compara analyses available (an analysis defines the type of comparative data).
GET info/compara/species_sets/:method List all collections of species analysed with the specified compara method.
GET info/comparas Lists all available comparative genomics databases and their data release.
GET info/data Shows the data releases available on this REST server. May return more than one release (unfrequent non-standard Ensembl configuration).
GET info/external_dbs/:species Lists all available external sources for a species.
GET info/ping Checks if the service is alive.
GET info/rest Shows the current version of the Ensembl REST API.
GET info/software Shows the current version of the Ensembl API used by the REST server.
GET info/species Lists all available species, their aliases, available adaptor groups and data release.

Lookup

ResourceDescription
GET lookup/id/:id Find the species and database for a single identifier
POST lookup/id/ Find the species and database for several identifiers. IDs that are not found are returned with no data.
GET lookup/symbol/:species/:symbol Find the species and database for a symbol in a linked external database
POST lookup/symbol/:species/:symbol Find the species and database for a set of symbols in a linked external database. Unknown symbols are omitted from the response.

Mapping

ResourceDescription
GET map/cdna/:id/:region Convert from cDNA coordinates to genomic coordinates. Output reflects forward orientation coordinates as returned from the Ensembl API.
GET map/cds/:id/:region Convert from CDS coordinates to genomic coordinates. Output reflects forward orientation coordinates as returned from the Ensembl API.
GET map/:species/:asm_one/:region/:asm_two Convert the co-ordinates of one assembly to another
GET map/translation/:id/:region Convert from protein (translation) coordinates to genomic coordinates. Output reflects forward orientation coordinates as returned from the Ensembl API.

Ontologies and Taxonomy

ResourceDescription
GET ontology/ancestors/:id Reconstruct the entire ancestry of a term from is_a and part_of relationships
GET ontology/ancestors/chart/:id Reconstruct the entire ancestry of a term from is_a and part_of relationships.
GET ontology/descendants/:id Find all the terms descended from a given term. By default searches are conducted within the namespace of the given identifier
GET ontology/id/:id Search for an ontological term by its namespaced identifier
GET ontology/name/:name Search for a list of ontological terms by their name
GET taxonomy/classification/:id Return the taxonomic classification of a taxon node
GET taxonomy/id/:id Search for a taxonomic term by its identifier or name
GET taxonomy/name/:name Search for a taxonomic id by a non-scientific name

Overlap

ResourceDescription
GET overlap/id/:id Retrieves features (e.g. genes, transcripts, variations etc.) that overlap a region defined by the given identifier.
GET overlap/region/:species/:region Retrieves multiple types of features for a given region.
GET overlap/translation/:id Retrieve features related to a specific Translation as described by its stable ID (e.g. domains, variations).

Regulation

ResourceDescription
GET regulatory/:species/:id Returns a RegulatoryFeature given its stable ID (e.g. ENSR00001348195)

Sequences

ResourceDescription
GET sequence/id/:id Request multiple types of sequence by stable identifier.
GET sequence/region/:species/:region Returns the genomic sequence of the specified region of the given species.

Variation

ResourceDescription
GET variation/:species/:id Uses a variation identifier (e.g. rsID) to return the variation features
GET vep/:species/id/:id Fetch variant consequences based on a variation identifier
POST vep/:species/id/ Fetch variant consequences for multiple ids
GET vep/:species/region/:region/:allele/ Fetch variant consequences
POST vep/:species/region/ Fetch variant consequences for multiple regions