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Ensembl REST API Endpoints

Archive

ResourceDescription
GET archive/id/:id Uses the given identifier to return the archived sequence

Comparative Genomics

ResourceDescription
GET alignment/region/:species/:region Retrieves genomic alignments as separate blocks based on its location
GET genetree/id/:id Retrieves Gene Tree dumps for a given Gene Tree stable identifier
GET genetree/member/id/:id Retrieves the Gene Tree that contains the given stable identifier
GET genetree/member/symbol/:species/:symbol Retrieves a Gene Tree containing the Gene identified by the given symbol
GET homology/id/:id Retrieves homology information by ensembl gene id
GET homology/symbol/:species/:symbol Retrieves homology information by symbol

Cross References

ResourceDescription
GET xrefs/id/:id Perform lookups of Ensembl Identifiers and retrieve their external cross 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
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).

Features

ResourceDescription
GET feature/id/:id Uses the given identifier as a way of indicating the Slice of features required. All returned features will overlap the given feature
GET feature/region/:species/:region Retrieves multiple types of features for a given region
GET feature/translation/:id Uses the given identifier to return translation related features.

Information

ResourceDescription
GET assembly/info/:species Returns information about the current available assemblies in this given species
GET assembly/info/:species/:region_name Returns information about the given toplevel sequence region given to this endpoint
GET info/analysis/:species Lists the available analyses by logic name and the database type those logic names are found in.
GET info/biotypes/:species Lists all available biotypes for the given species. These can be used to limit gene and transcript retrieval.
GET info/compara/methods Returns the method types available for this compara database. Methods can be used in endpoints to specify the type of data comparative data required.
GET info/compara/species_sets/:method Returns the all the species sets linked to this method. If a species set is not named the species names will be made available as an additional array of unnamed species sets
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. Can return more than one release but this is rare (and non-standard Ensembl configuration)
GET info/external_dbs/:species Lists the external database entries in the specified species. External dbs can be specified to restrict symbol lookups to a single or range of sources.
GET info/ping Pings the first available DBAdaptor to see if the service is still active
GET info/rest Shows the current version of the REST API
GET info/software Shows the current version of the Ensembl API
GET info/species Lists all available species, their aliases, available adaptor groups and data release

Lookup

ResourceDescription
GET lookup/id/:id Query for an identifier's location in the available Ensembl databases
GET lookup/symbol/:species/:symbol Query for a symbol in the available Ensembl databases

Mapping

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

Ontologies and Taxonomy

ResourceDescription
GET ontology/ancestors/:id Find all ancestors, all terms above, belonging to a given term. It is possible to restrict the search to a single ontology so as to help when terms are shared between ontologies e.g. EFO. By default searches are conducted within the namespace of the given identifier
GET ontology/ancestors/chart/:id Reconstruct the entire ancestory of a term from is_a and part_of relationships.
GET ontology/descendents/:id Find all descendents, all terms below, belonging to a given term. It is possible to restrict the search to a single ontology so as to help when terms are shared between ontologies e.g. EFO. 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 and an optional ontology
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

Sequences

ResourceDescription
GET sequence/id/:id Query for multiple types of Sequence by its stable identifier
GET sequence/region/:species/:region Query for a region of genomic sequence based on its location

Variation

ResourceDescription
GET vep/:species/:region/:allele/consequences Fetch variant consequences
GET vep/:species/id/:id/consequences Fetch variant consequences based on a variation identifier