Ensembl REST API Coverage

The list of Ensembl REST API endpoints can be found at https://rest.ensembl.org/. Below you will find the current coverage of Ensembl REST API endpoints by {ensemblr}.

Coverage

Ensembl REST API Section Coverage
Archive 2/2
Comparative genomics 0/12
Cross references 2/3
eQTL 3/3
Information 10/26
Linkage disequilibrium 3/3
Lookup 0/4
Mapping 0/4
Ontologies and taxonomy 0/8
Overlap 0/3
Phenotype annotations 0/4
Regulation 0/7
Sequence 0/4
Transcript Haplotypes 0/1
VEP 0/6
Variation 0/6
Variation GA4GH 0/22

Archive

Ensembl REST API {ensemblr} API Description
GET archive/id/:id get_id() Get details about an Ensembl identifier.
POST archive/id Get details about an Ensembl identifier.

Cross references

Ensembl REST API {ensemblr} API Description
GET xrefs/symbol/:species/:symbol
GET xrefs/id/:id get_xrefs_by_ensembl_id()
GET xrefs/name/:species/:name get_xrefs_by_gene()

eQTL

Ensembl REST API {ensemblr} API Description
GET eqtl/id/:species/:stable_id get_eqtl_pval_by_gene() Retrieve eQTLs associated with queried gene.
GET eqtl/variant_name/:species/:variant_name get_eqtl_pval_by_variant() Retrieve genes eQTL associated with queried variant.
GET eqtl/tissue/:species get_eqtl_tissues() Returns all tissues currently available in the eQTL database.

Information

Ensembl REST API {ensemblr} API Description
GET info/analysis/:species get_analyses() Gets a table of analyses involved in the generation of data for the different Ensembl databases.
GET info/assembly/:species get_assemblies() get_toplevel_sequences() get_karyotypes() get_cytogenetic_bands() Genome assembly level information, such as toplevel sequences, karyotype and cytogenetic bands.
GET info/assembly/:species/:region_name get_toplevel_sequence_info() Get a few extra details about a toplevel sequence.
GET info/biotypes/:species
GET info/biotypes/groups/:group/:object_type
GET info/biotypes/name/:name/:object_type
GET info/compara/methods
GET info/compara/species_sets/:method
GET info/comparas
GET info/data get_data_versions() Get data release version(s) available on the Ensembl REST server.
GET info/eg_version get_ensembl_genomes_version() Get Ensembl Genomes database version.
GET info/external_dbs/:species
GET info/divisions get_divisions() Retrieve Ensembl divisions.
GET info/genomes/:genome_name
GET info/genomes/accession/:accession
GET info/genomes/assembly/:assembly_id
GET info/genomes/division/:division_name
GET info/genomes/taxonomy/:taxon_name
GET info/ping
GET info/rest get_rest_version() Retrieve the current version of the Ensembl REST API.
GET info/software get_software_version() Retrieve the Perl API version.
GET info/species get_species() Retrieves species-level information.
GET info/variation/:species get_variation_sources() Retrieves variant sources, i.e. a list of databases used by Ensembl for obtaining variant information.
GET info/variation/consequence_types get_variant_consequences() Retrieves variant consequence types.
GET info/variation/populations/:species:/:population_name get_individuals() Retrieves individual-level information.
GET info/variation/populations/:species get_populations() Retrieves population-level information.

Linkage disequilibrium

Ensembl REST API {ensemblr} API Description
GET ld/:species/:id/:population_name get_ld_variants_by_window() Gets linkage disequilibrium data by genomic window centred on queried variants.
GET ld/:species/pairwise/:id1/:id2 get_ld_variants_by_pair() Gets linkage disequilibrium data for pairs of queried variants.
GET ld/:species/region/:region/:population_name get_ld_variants_by_range() Gets linkage disequilibrium data by genomic range.

Lookup

Ensembl REST API {ensemblr} API Description
GET lookup/id/:id
POST lookup/id
GET lookup/symbol/:species/:symbol
POST lookup/symbol/:species/:symbol

Mapping

Ensembl REST API {ensemblr} API Description
GET map/cdna/:id/:region
GET map/cds/:id/:region
GET map/:species/:asm_one/:region/:asm_two
GET map/translation/:id/:region

Ontologies and taxonomy

Ensembl REST API {ensemblr} API Description
GET ontology/ancestors/:id
GET ontology/ancestors/chart/:id
GET ontology/descendants/:id
GET ontology/id/:id
GET ontology/name/:name
GET taxonomy/classification/:id
GET taxonomy/id/:id
GET taxonomy/name/:name

Overlap

Ensembl REST API {ensemblr} API Description
GET overlap/id/:id
GET overlap/region/:species/:region
GET overlap/translation/:id

Phenotype annotations

Ensembl REST API {ensemblr} API Description
GET /phenotype/accession/:species/:accession
GET /phenotype/gene/:species/:gene
GET /phenotype/region/:species/:region
GET /phenotype/term/:species/:term

Sequence

Ensembl REST API {ensemblr} API Description
GET sequence/id/:id
POST sequence/id
GET sequence/region/:species/:region
POST sequence/region/:species

Transcript haplotypes

Ensembl REST API {ensemblr} API Description
GET transcript_haplotypes/:species/:id