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 is_ensembl_reachable() Check access to the Ensembl REST API server.
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 — —