VectorBase REST API Endpoints

Archive

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

Comparative Genomics

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

Cross References

ResourceDescription
GET /rest/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 /rest/xrefs/id/:id Perform lookups of Ensembl Identifiers and retrieve their external references in other databases
GET /rest/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 /rest/info/analysis/:species List the names of analyses involved in generating Ensembl data.
GET /rest/info/assembly/:species List the currently available assemblies for a species, along with toplevel sequences, chromosomes and cytogenetic bands.
GET /rest/info/assembly/:species/:region_name Returns information about the specified toplevel sequence region for the given species.
GET /rest/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 /rest/info/compara/methods List all compara analyses available (an analysis defines the type of comparative data).
GET /rest/info/compara/species_sets/:method List all collections of species analysed with the specified compara method.
GET /rest/info/comparas Lists all available comparative genomics databases and their data release.
GET /rest/info/data Shows the data releases available on this REST server. May return more than one release (unfrequent non-standard Ensembl configuration).
GET /rest/info/external_dbs/:species Lists all available external sources for a species.
GET /rest/info/ping Checks if the service is alive.
GET /rest/info/rest Shows the current version of the Ensembl REST API.
GET /rest/info/software Shows the current version of the Ensembl API used by the REST server.
GET /rest/info/species Lists all available species, their aliases, available adaptor groups and data release.
GET /rest/info/variation/:species List the variation sources used in Ensembl for a species.
GET /rest/info/variation/consequence_types Lists all variant consequence types.
GET /rest/info/variation/populations/:species List all populations for a species

Linkage Disequilibrium

ResourceDescription
GET /rest/ld/:species/:id/:population_name Computes and returns LD values between the given variant and all other variants in a window centered around the given variant. The window size is set to 500 kb.
GET /rest/ld/:species/pairwise/:id1/:id2 Computes and returns LD values between the given variants.
GET /rest/ld/:species/region/:region/:population_name Computes and returns LD values between all pairs of variants in the defined region.

Lookup

ResourceDescription
GET /rest/lookup/id/:id Find the species and database for a single identifier e.g. gene, transcript, protein
POST /rest/lookup/id Find the species and database for several identifiers. IDs that are not found are returned with no data.
GET /rest/lookup/symbol/:species/:symbol Find the species and database for a symbol in a linked external database
POST /rest/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 /rest/map/cdna/:id/:region Convert from cDNA coordinates to genomic coordinates. Output reflects forward orientation coordinates as returned from the Ensembl API.
GET /rest/map/cds/:id/:region Convert from CDS coordinates to genomic coordinates. Output reflects forward orientation coordinates as returned from the Ensembl API.
GET /rest/map/:species/:asm_one/:region/:asm_two Convert the co-ordinates of one assembly to another
GET /rest/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 /rest/ontology/ancestors/:id Reconstruct the entire ancestry of a term from is_a and part_of relationships
GET /rest/ontology/ancestors/chart/:id Reconstruct the entire ancestry of a term from is_a and part_of relationships.
GET /rest/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 /rest/ontology/id/:id Search for an ontological term by its namespaced identifier
GET /rest/ontology/name/:name Search for a list of ontological terms by their name
GET /rest/taxonomy/classification/:id Return the taxonomic classification of a taxon node
GET /rest/taxonomy/id/:id Search for a taxonomic term by its identifier or name
GET /rest/taxonomy/name/:name Search for a taxonomic id by a non-scientific name

Overlap

ResourceDescription
GET /rest/overlap/id/:id Retrieves features (e.g. genes, transcripts, variants and more) that overlap a region defined by the given identifier.
GET /rest/overlap/region/:species/:region Retrieves features (e.g. genes, transcripts, variants and more) that overlap a given region.
GET /rest/overlap/translation/:id Retrieve features related to a specific Translation as described by its stable ID (e.g. domains, variants).

Phenotype annotations

ResourceDescription
GET /rest//phenotype/gene/:species/:gene Return phenotype annotations for a given gene.
GET /rest//phenotype/region/:species/:region Return phenotype annotations that overlap a given genomic region.

Regulation

ResourceDescription
GET /rest/regulatory/species/:species/microarray/:microarray/vendor/:vendor Returns information about a specific microarray
GET /rest/regulatory/species/:species/microarray Returns information about all microarrays available for the given species
GET /rest/regulatory/species/:species/microarray/:microarray/probe/:probe Returns information about a specific probe from a microarray
GET /rest/regulatory/species/:species/microarray/:microarray/probe_set/:probe_set Returns information about a specific probe_set from a microarray

Sequence

ResourceDescription
GET /rest/sequence/id/:id Request multiple types of sequence by stable identifier. Supports feature masking and expand options.
POST /rest/sequence/id Request multiple types of sequence by a stable identifier list.
GET /rest/sequence/region/:species/:region Returns the genomic sequence of the specified region of the given species. Supports feature masking and expand options.
POST /rest/sequence/region/:species Request multiple types of sequence by a list of regions.

Variation

ResourceDescription
GET /rest/variant_recoder/:species/:id Translate a variant identifier or HGVS notation to all possible variant IDs and HGVS
POST /rest/variant_recoder/:species Translate a list of variant identifiers or HGVS notations to all possible variant IDs and HGVS
GET /rest/variation/:species/:id Uses a variant identifier (e.g. rsID) to return the variation features including optional genotype, phenotype and population data
GET /rest/variation/:species/pmcid/:pmcid Fetch variants by publication using PubMed Central reference number (PMCID)
GET /rest/variation/:species/pmid/:pmid Fetch variants by publication using PubMed reference number (PMID)
POST /rest/variation/:species/ Uses a list of variant identifiers (e.g. rsID) to return the variation features including optional genotype, phenotype and population data