Archive | |
| Resource | Description |
|---|---|
| GET /rest/archive/id/:id | Uses the given identifier to return its latest version |
| POST /rest/archive/id | Retrieve the latest version for a set of identifiers |
Comparative Genomics | |
| Resource | Description |
| 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 | |
| Resource | Description |
| 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 | |
| Resource | Description |
| 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/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 /rest/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 /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:/:population_name | List all individuals for a population from a species |
| GET /rest/info/variation/populations/:species | List all populations for a species |
Linkage Disequilibrium | |
| Resource | Description |
| 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 | |
| Resource | Description |
| 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 | |
| Resource | Description |
| 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 | |
| Resource | Description |
| 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 | |
| Resource | Description |
| 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 | |
| Resource | Description |
| 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 | |
| Resource | Description |
| GET /rest/regulatory/species/:species/microarray/:microarray/vendor/:vendor | Returns information about a specific microarray |
| GET /rest/species/:species/binding_matrix/:binding_matrix_stable_id/ | Return the specified binding matrix |
| 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 | |
| Resource | Description |
| GET /rest/sequence/proteome/:species | Dowbload whole proteome peptides sequence for a given speciess. |
| 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 | |
| Resource | Description |
| 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 |
