Ensembl REST API Endpoints
Archive | |
| Resource | Description |
|---|---|
| GET archive/id/:id | Uses the given identifier to return its latest version |
| POST archive/id | Retrieve the latest version for a set of identifiers |
Comparative Genomics | |
| Resource | Description |
| GET alignment/region/:species/:region | Retrieves genomic alignments as separate blocks based on a region and species |
| GET homology/id/:species/:id | Retrieves homology information (orthologs) by Ensembl gene id |
| GET homology/symbol/:species/:symbol | Retrieves homology information (orthologs) by symbol |
Cross References | |
| Resource | Description |
| 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 | |
| Resource | Description |
| 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, along with toplevel sequences, chromosomes and cytogenetic bands. |
| 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/biotypes/groups/:group/:object_type | Without argument the list of available biotype groups is returned. With :group argument provided, list the properties of biotypes within that group. Object type (gene or transcript) can be provided for filtering. |
| GET info/biotypes/name/:name/:object_type | List the properties of biotypes with a given name. Object type (gene or transcript) can be provided for filtering. |
| 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. DEPRECATED: use info/genomes/division instead. |
| 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. |
| GET info/variation/:species | List the variation sources used in Ensembl for a species. |
| GET info/variation/consequence_types | Lists all variant consequence types. |
| GET info/variation/populations/:species:/:population_name | List all individuals for a population from a species |
| GET info/variation/populations/:species | List all populations for a species |
Linkage Disequilibrium | |
| Resource | Description |
| GET 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 ld/:species/pairwise/:id1/:id2 | Computes and returns LD values between the given variants. |
| GET ld/:species/region/:region/:population_name | Computes and returns LD values between all pairs of variants in the defined region. |
Lookup | |
| Resource | Description |
| GET lookup/id/:id | Find the species and database for a single identifier e.g. gene, transcript, protein |
| 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 | |
| Resource | Description |
| 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 | |
| Resource | Description |
| 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 | |
| Resource | Description |
| GET overlap/id/:id | Retrieves features (e.g. genes, transcripts, variants and more) that overlap a region defined by the given identifier. |
| GET overlap/region/:species/:region | Retrieves features (e.g. genes, transcripts, variants and more) that overlap a given region. |
| GET overlap/translation/:id | Retrieve features related to a specific Translation as described by its stable ID (e.g. domains, variants). |
Phenotype annotations | |
| Resource | Description |
| GET /phenotype/accession/:species/:accession | Return phenotype annotations for genomic features given a phenotype ontology accession |
| GET /phenotype/gene/:species/:gene | Return phenotype annotations for a given gene. |
| GET /phenotype/region/:species/:region | Return phenotype annotations that overlap a given genomic region. |
| GET /phenotype/term/:species/:term | Return phenotype annotations for genomic features given a phenotype ontology term |
Regulation | |
| Resource | Description |
| GET regulatory/species/:species/microarray/:microarray/vendor/:vendor | Returns information about a specific microarray |
| GET regulatory/species/:species/epigenome | Returns information about all epigenomes available for the given species |
| GET species/:species/binding_matrix/:binding_matrix_stable_id/ | Return the specified binding matrix |
| GET regulatory/species/:species/microarray | Returns information about all microarrays available for the given species |
| GET regulatory/species/:species/microarray/:microarray/probe/:probe | Returns information about a specific probe from a microarray |
| GET regulatory/species/:species/microarray/:microarray/probe_set/:probe_set | Returns information about a specific probe_set from a microarray |
| GET regulatory/species/:species/id/:id | Returns a RegulatoryFeature given its stable ID (e.g. ENSR00000082023) |
Sequence | |
| Resource | Description |
| GET sequence/id/:id | Request multiple types of sequence by stable identifier. Supports feature masking and expand options. |
| POST sequence/id | Request multiple types of sequence by a stable identifier list. |
| GET sequence/region/:species/:region | Returns the genomic sequence of the specified region of the given species. Supports feature masking and expand options. |
| POST sequence/region/:species | Request multiple types of sequence by a list of regions. |
Transcript Haplotypes | |
| Resource | Description |
| GET transcript_haplotypes/:species/:id | Computes observed transcript haplotype sequences based on phased genotype data |
VEP | |
| Resource | Description |
| GET vep/:species/hgvs/:hgvs_notation | Fetch variant consequences based on a HGVS notation |
| POST vep/:species/hgvs | Fetch variant consequences for multiple HGVS notations |
| GET vep/:species/id/:id | Fetch variant consequences based on a variant 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 |
Variation | |
| Resource | Description |
| GET variant_recoder/:species/:id | Translate a variant identifier, HGVS notation or genomic SPDI notation to all possible variant IDs, HGVS and genomic SPDI |
| POST variant_recoder/:species | Translate a list of variant identifiers, HGVS notations or genomic SPDI notations to all possible variant IDs, HGVS and genomic SPDI |
| GET variation/:species/:id | Uses a variant identifier (e.g. rsID) to return the variation features including optional genotype, phenotype and population data |
| GET variation/:species/pmcid/:pmcid | Fetch variants by publication using PubMed Central reference number (PMCID) |
| GET variation/:species/pmid/:pmid | Fetch variants by publication using PubMed reference number (PMID) |
| POST variation/:species/ | Uses a list of variant identifiers (e.g. rsID) to return the variation features including optional genotype, phenotype and population data |
Variation GA4GH | |
| Resource | Description |
| GET ga4gh/beacon | Return Beacon information |
| GET ga4gh/beacon/query | Return the Beacon response for allele information |
| POST ga4gh/beacon/query | Return the Beacon response for allele information |
| GET ga4gh/features/:id | Return the GA4GH record for a specific sequence feature given its identifier |
| POST ga4gh/features/search | Return a list of sequence annotation features in GA4GH format |
| POST ga4gh/callsets/search | Return a list of sets of genotype calls for specific samples in GA4GH format |
| GET ga4gh/callsets/:id | Return the GA4GH record for a specific CallSet given its identifier |
| POST ga4gh/datasets/search | Return a list of datasets in GA4GH format |
| GET ga4gh/datasets/:id | Return the GA4GH record for a specific dataset given its identifier |
| POST ga4gh/featuresets/search | Return a list of feature sets in GA4GH format |
| GET ga4gh/featuresets/:id | Return the GA4GH record for a specific featureSet given its identifier |
| GET ga4gh/variants/:id | Return the GA4GH record for a specific variant given its identifier. |
| POST ga4gh/variantannotations/search | Return variant annotation information in GA4GH format for a region on a reference sequence |
| POST ga4gh/variants/search | Return variant call information in GA4GH format for a region on a reference sequence |
| POST ga4gh/variantsets/search | Return a list of variant sets in GA4GH format |
| GET ga4gh/variantsets/:id | Return the GA4GH record for a specific VariantSet given its identifier |
| POST ga4gh/references/search | Return a list of reference sequences in GA4GH format |
| GET ga4gh/references/:id | Return data for a specific reference in GA4GH format by id |
| POST ga4gh/referencesets/search | Return a list of reference sets in GA4GH format |
| GET ga4gh/referencesets/:id | Return data for a specific reference set in GA4GH format |
| POST ga4gh/variantannotationsets/search | Return a list of annotation sets in GA4GH format |
| GET ga4gh/variantannotationsets/:id | Return meta data for a specific annotation set in GA4GH format |