---
title: "Ensembl REST API Coverage"
output: rmarkdown::html_vignette
vignette: >
  %\VignetteIndexEntry{Ensembl REST API Coverage}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---

```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)
```

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](https://rest.ensembl.org/documentation/info/archive_id_get)  | `get_id()`       | Get details about an Ensembl identifier. |
| [POST archive/id](https://rest.ensembl.org/documentation/info/archive_id_post)     | ---       | Get details about an Ensembl identifier. |

## Comparative genomics

| Ensembl REST API                                    | `{ensemblr}` API | Description |
| --------------------------------------------------- | ---------------- | ----------- |
| [GET cafe/genetree/id/:id](https://rest.ensembl.org/documentation/info/cafe_tree)                            | --- | --- |
| [GET cafe/genetree/member/id/:id](https://rest.ensembl.org/documentation/info/cafe_tree_member_id)                     | --- | --- |
| [GET cafe/genetree/member/symbol/:species/:symbol](https://rest.ensembl.org/documentation/info/cafe_tree_member_symbol)    | --- | --- |
| [GET family/id/:id](https://rest.ensembl.org/documentation/info/family)                                   | --- | --- |
| [GET family/member/id/:id](https://rest.ensembl.org/documentation/info/family_member_id)                            | --- | --- |
| [GET family/member/symbol/:species/:symbol](https://rest.ensembl.org/documentation/info/family_member_symbol)           | --- | --- |
| [GET genetree/id/:id](https://rest.ensembl.org/documentation/info/genetree)                                 | --- | --- |
| [GET genetree/member/id/:id](https://rest.ensembl.org/documentation/info/genetree_member_id)                          | --- | --- |
| [GET genetree/member/symbol/:species/:symbol](https://rest.ensembl.org/documentation/info/genetree_member_symbol)         | --- | --- |
| [GET alignment/region/:species/:region](https://rest.ensembl.org/documentation/info/genomic_alignment_region)               | --- | --- |
| [GET homology/id/:id](https://rest.ensembl.org/documentation/info/homology_ensemblgene)                                 | --- | --- |
| [GET homology/symbol/:species/:symbol](https://rest.ensembl.org/documentation/info/homology_symbol)                | --- | --- |

## Cross references

| Ensembl REST API | `{ensemblr}` API | Description |
| ---------------- | ---------------- | ----------- |
| [GET xrefs/symbol/:species/:symbol](https://rest.ensembl.org/documentation/info/xref_external) | --- | --- |
| [GET xrefs/id/:id](https://rest.ensembl.org/documentation/info/xref_id) | `get_xrefs_by_ensembl_id()` | --- |
| [GET xrefs/name/:species/:name](https://rest.ensembl.org/documentation/info/xref_name) | `get_xrefs_by_gene()` | --- |

## eQTL

| Ensembl REST API | `{ensemblr}` API | Description |
| ---------------- | ---------------- | ----------- |
| [GET eqtl/id/:species/:stable_id](https://rest.ensembl.org/documentation/info/species_id) | `get_eqtl_pval_by_gene()` | Retrieve eQTLs associated with queried gene. |
| [GET eqtl/variant_name/:species/:variant_name](https://rest.ensembl.org/documentation/info/species_variant) | `get_eqtl_pval_by_variant()` | Retrieve genes eQTL associated with queried variant. |
| [GET eqtl/tissue/:species](https://rest.ensembl.org/documentation/info/tissues) | `get_eqtl_tissues()` | Returns all tissues currently available in the eQTL database. |

## Information

| Ensembl REST API | `{ensemblr}` API | Description |
| ---------------- | ---------------- | ----------- |
| [GET info/analysis/:species](https://rest.ensembl.org/documentation/info/analysis) | `get_analyses()` | Gets a table of analyses involved in the generation of data for the different Ensembl databases. |
| [GET info/assembly/:species](https://rest.ensembl.org/documentation/info/assembly_info) | `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](https://rest.ensembl.org/documentation/info/assembly_stats) | `get_toplevel_sequence_info()` | Get a few extra details about a toplevel sequence. |
| [GET info/biotypes/:species](https://rest.ensembl.org/documentation/info/biotypes) | --- | --- |
| [GET info/biotypes/groups/:group/:object_type](https://rest.ensembl.org/documentation/info/biotypes_groups) | --- | --- |
| [GET info/biotypes/name/:name/:object_type](https://rest.ensembl.org/documentation/info/biotypes_name) | --- | --- |
| [GET info/compara/methods](https://rest.ensembl.org/documentation/info/compara_methods) | --- | --- |
| [GET info/compara/species_sets/:method](https://rest.ensembl.org/documentation/info/compara_species_sets) | --- | --- |
| [GET info/comparas](https://rest.ensembl.org/documentation/info/comparas) | --- | --- |
| [GET info/data](https://rest.ensembl.org/documentation/info/data) | `get_data_versions()` | Get data release version(s) available on the Ensembl REST server. |
| [GET info/eg_version](https://rest.ensembl.org/documentation/info/eg_version) | `get_ensembl_genomes_version()` | Get Ensembl Genomes database version. |
| [GET info/external_dbs/:species](https://rest.ensembl.org/documentation/info/external_dbs) | --- | --- |
| [GET info/divisions](https://rest.ensembl.org/documentation/info/info_divisions) | `get_divisions()` | Retrieve Ensembl divisions. |
| [GET info/genomes/:genome_name](https://rest.ensembl.org/documentation/info/info_genome) | --- | --- |
| [GET info/genomes/accession/:accession](https://rest.ensembl.org/documentation/info/info_genomes_accession) | --- | --- |
| [GET info/genomes/assembly/:assembly_id](https://rest.ensembl.org/documentation/info/info_genomes_assembly) | --- | --- |
| [GET info/genomes/division/:division_name](https://rest.ensembl.org/documentation/info/info_genomes_division) | --- | --- |
| [GET info/genomes/taxonomy/:taxon_name](https://rest.ensembl.org/documentation/info/info_genomes_taxonomy) | --- | --- |
| [GET info/ping](https://rest.ensembl.org/documentation/info/ping) | `is_ensembl_reachable()` | Check access to the Ensembl REST API server. |
| [GET info/rest](https://rest.ensembl.org/documentation/info/rest) | `get_rest_version()` | Retrieve the current version of the Ensembl REST API. |
| [GET info/software](https://rest.ensembl.org/documentation/info/software) | `get_software_version()` | Retrieve the Perl API version. |
| [GET info/species](https://rest.ensembl.org/documentation/info/species) | `get_species()` | Retrieves species-level information. |
| [GET info/variation/:species](https://rest.ensembl.org/documentation/info/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](https://rest.ensembl.org/documentation/info/variation_consequence_types) | `get_variant_consequences()` | Retrieves variant consequence types. |
| [GET info/variation/populations/:species:/:population_name](https://rest.ensembl.org/documentation/info/variation_population_name) | `get_individuals()` | Retrieves individual-level information. |
| [GET info/variation/populations/:species](https://rest.ensembl.org/documentation/info/variation_populations) | `get_populations()` | Retrieves population-level information. |

## Linkage disequilibrium

| Ensembl REST API | `{ensemblr}` API | Description |
| ---------------- | ---------------- | ----------- |
| [GET ld/:species/:id/:population_name](https://rest.ensembl.org/documentation/info/ld_id_get) | `get_ld_variants_by_window()` | Gets linkage disequilibrium data by genomic window centred on queried variants. |
| [GET ld/:species/pairwise/:id1/:id2](https://rest.ensembl.org/documentation/info/ld_pairwise_get) | `get_ld_variants_by_pair()` | Gets linkage disequilibrium data for pairs of queried variants. |
| [GET ld/:species/region/:region/:population_name](https://rest.ensembl.org/documentation/info/ld_region_get) | `get_ld_variants_by_range()` | Gets linkage disequilibrium data by genomic range. |

## Lookup

| Ensembl REST API | `{ensemblr}` API | Description |
| ---------------- | ---------------- | ----------- |
| [GET lookup/id/:id](https://rest.ensembl.org/documentation/info/lookup) | --- | --- |
| [POST lookup/id](https://rest.ensembl.org/documentation/info/lookup_post) | --- | --- |
| [GET lookup/symbol/:species/:symbol](https://rest.ensembl.org/documentation/info/symbol_lookup) | --- | --- |
| [POST lookup/symbol/:species/:symbol](https://rest.ensembl.org/documentation/info/symbol_post) | --- | --- |

## Mapping

| Ensembl REST API | `{ensemblr}` API | Description |
| ---------------- | ---------------- | ----------- |
| [GET map/cdna/:id/:region](https://rest.ensembl.org/documentation/info/assembly_cdna) | --- | --- |
| [GET map/cds/:id/:region](https://rest.ensembl.org/documentation/info/assembly_cds) | --- | --- |
| [GET map/:species/:asm_one/:region/:asm_two](https://rest.ensembl.org/documentation/info/assembly_map) | --- | --- |
| [GET map/translation/:id/:region](https://rest.ensembl.org/documentation/info/assembly_translation) | --- | --- |

## Ontologies and taxonomy

| Ensembl REST API | `{ensemblr}` API | Description |
| ---------------- | ---------------- | ----------- |
| [GET ontology/ancestors/:id](https://rest.ensembl.org/documentation/info/ontology_ancestors) | --- | --- |
| [GET ontology/ancestors/chart/:id](https://rest.ensembl.org/documentation/info/ontology_ancestors_chart) | --- | --- |
| [GET ontology/descendants/:id](https://rest.ensembl.org/documentation/info/ontology_descendants) | --- | --- |
| [GET ontology/id/:id](https://rest.ensembl.org/documentation/info/ontology_id) | --- | --- |
| [GET ontology/name/:name](https://rest.ensembl.org/documentation/info/taxonomy_classification) | --- | --- |
| [GET taxonomy/classification/:id](https://rest.ensembl.org/documentation/info/taxonomy_classification) | --- | --- |
| [GET taxonomy/id/:id](https://rest.ensembl.org/documentation/info/taxonomy_id) | --- | --- |
| [GET taxonomy/name/:name](https://rest.ensembl.org/documentation/info/taxonomy_name) | --- | --- |

## Overlap

| Ensembl REST API | `{ensemblr}` API | Description |
| ---------------- | ---------------- | ----------- |
| [GET overlap/id/:id](https://rest.ensembl.org/documentation/info/overlap_id) | --- | --- |
| [GET overlap/region/:species/:region](https://rest.ensembl.org/documentation/info/overlap_region) | --- | --- |
| [GET overlap/translation/:id](https://rest.ensembl.org/documentation/info/overlap_translation) | --- | --- |

## Phenotype annotations

| Ensembl REST API | `{ensemblr}` API | Description |
| ---------------- | ---------------- | ----------- |
| [GET /phenotype/accession/:species/:accession](https://rest.ensembl.org/documentation/info/phenotype_accession) | --- | --- |
| [GET /phenotype/gene/:species/:gene](https://rest.ensembl.org/documentation/info/phenotype_gene) | --- | --- |
| [GET /phenotype/region/:species/:region](https://rest.ensembl.org/documentation/info/phenotype_region) | --- | --- |
| [GET /phenotype/term/:species/:term](https://rest.ensembl.org/documentation/info/phenotype_term) | --- | --- |

## Regulation

| Ensembl REST API | `{ensemblr}` API | Description |
| ---------------- | ---------------- | ----------- |
| [GET regulatory/species/:species/microarray/:microarray/vendor/:vendor](https://rest.ensembl.org/documentation/info/array)	 | --- | --- |
| [GET regulatory/species/:species/epigenome](https://rest.ensembl.org/documentation/info/fetch_all_epigenomes) | --- | --- |
| [GET species/:species/binding_matrix/:binding_matrix_stable_id/](https://rest.ensembl.org/documentation/info/get_binding_matrix) | --- | --- |
| [GET regulatory/species/:species/microarray](https://rest.ensembl.org/documentation/info/list_all_microarrays) | --- | --- |
| [GET regulatory/species/:species/microarray/:microarray/probe/:probe](https://rest.ensembl.org/documentation/info/probe) | --- | --- |
| [GET regulatory/species/:species/microarray/:microarray/probe_set/:probe_set](https://rest.ensembl.org/documentation/info/probe_set) | --- | --- |
| [GET regulatory/species/:species/id/:id](https://rest.ensembl.org/documentation/info/regulatory_id) | --- | --- |

## Sequence

| Ensembl REST API | `{ensemblr}` API | Description |
| ---------------- | ---------------- | ----------- |
| [GET sequence/id/:id](https://rest.ensembl.org/documentation/info/sequence_id) | --- | --- |
| [POST sequence/id](https://rest.ensembl.org/documentation/info/sequence_id_post) | --- | --- |
| [GET sequence/region/:species/:region](https://rest.ensembl.org/documentation/info/sequence_region) | --- | --- |
| [POST sequence/region/:species](https://rest.ensembl.org/documentation/info/sequence_region_post) | --- | --- |

## Transcript haplotypes

| Ensembl REST API | `{ensemblr}` API | Description |
| ---------------- | ---------------- | ----------- |
| [GET transcript_haplotypes/:species/:id](https://rest.ensembl.org/documentation/info/transcript_haplotypes_get) | --- | --- |

## VEP

| Ensembl REST API | `{ensemblr}` API | Description |
| ---------------- | ---------------- | ----------- |
| [GET vep/:species/hgvs/:hgvs_notation](https://rest.ensembl.org/documentation/info/vep_hgvs_get) | --- | --- |
| [POST vep/:species/hgvs](https://rest.ensembl.org/documentation/info/vep_hgvs_post) | --- | --- |
| [GET vep/:species/id/:id](https://rest.ensembl.org/documentation/info/vep_id_get) | --- | --- |
| [POST vep/:species/id](https://rest.ensembl.org/documentation/info/vep_id_post) | --- | --- |
| [GET vep/:species/region/:region/:allele/](https://rest.ensembl.org/documentation/info/vep_region_get) | --- | --- |
| [POST vep/:species/region](https://rest.ensembl.org/documentation/info/vep_region_post) | --- | --- |

## Variation

| Ensembl REST API | `{ensemblr}` API | Description |
| ---------------- | ---------------- | ----------- |
| [GET variant_recoder/:species/:id](https://rest.ensembl.org/documentation/info/variant_recoder) | --- | --- |
| [POST variant_recoder/:species](https://rest.ensembl.org/documentation/info/variant_recoder_post) | --- | --- |
| [GET variation/:species/:id](https://rest.ensembl.org/documentation/info/variation_id) | --- | --- |
| [GET variation/:species/pmcid/:pmcid](https://rest.ensembl.org/documentation/info/variation_pmcid_get) | --- | --- |
| [GET variation/:species/pmid/:pmid](https://rest.ensembl.org/documentation/info/variation_pmid_get) | --- | --- |
| [POST variation/:species/](https://rest.ensembl.org/documentation/info/variation_post) | --- | --- |

## Variation GA4GH

| Ensembl REST API | `{ensemblr}` API | Description |
| ---------------- | ---------------- | ----------- |
| [GET ga4gh/beacon](https://rest.ensembl.org/documentation/info/beacon_get) | --- | --- |
| [GET ga4gh/beacon/query](https://rest.ensembl.org/documentation/info/beacon_query_get) | --- | --- |
| [POST ga4gh/beacon/query](https://rest.ensembl.org/documentation/info/beacon_query_post) | --- | --- |
| [GET ga4gh/features/:id](https://rest.ensembl.org/documentation/info/features_id) | --- | --- |
| [POST ga4gh/features/search](https://rest.ensembl.org/documentation/info/features_post) | --- | --- |
| [POST ga4gh/callsets/search](POST ga4gh/callsets/search) | --- | --- |
| [GET ga4gh/callsets/:id](https://rest.ensembl.org/documentation/info/gacallset_id) | --- | --- |
| [POST ga4gh/datasets/search](https://rest.ensembl.org/documentation/info/gadataset) | --- | --- |
| [GET ga4gh/datasets/:id](https://rest.ensembl.org/documentation/info/gadataset_id) | --- | --- |
| [POST ga4gh/featuresets/search](https://rest.ensembl.org/documentation/info/gafeatureset) | --- | --- |
| [GET ga4gh/featuresets/:id](https://rest.ensembl.org/documentation/info/gafeatureset_id) | --- | --- |
| [GET ga4gh/variants/:id](https://rest.ensembl.org/documentation/info/gavariant_id) | --- | --- |
| [POST ga4gh/variantannotations/search](https://rest.ensembl.org/documentation/info/gavariantannotations) | --- | --- |
| [POST ga4gh/variants/search](https://rest.ensembl.org/documentation/info/gavariants) | --- | --- |
| [POST ga4gh/variantsets/search](https://rest.ensembl.org/documentation/info/gavariantset) | --- | --- |
| [GET ga4gh/variantsets/:id](https://rest.ensembl.org/documentation/info/gavariantset_id) | --- | --- |
| [POST ga4gh/references/search](https://rest.ensembl.org/documentation/info/references) | --- | --- |
| [GET ga4gh/references/:id](https://rest.ensembl.org/documentation/info/references_id) | --- | --- |
| [POST ga4gh/referencesets/search](https://rest.ensembl.org/documentation/info/referenceSets) | --- | --- |
| [GET ga4gh/referencesets/:id](https://rest.ensembl.org/documentation/info/referenceSets_id) | --- | --- |
| [POST ga4gh/variantannotationsets/search](https://rest.ensembl.org/documentation/info/VariantAnnotationSet) | --- | --- |
| [GET ga4gh/variantannotationsets/:id](https://rest.ensembl.org/documentation/info/VariantAnnotationSet_id) | --- | --- |