Tamara El Naboulsi edited this page
May 28, 2025·
74 revisions Ensembl REST Server Change LogPlease note all dates are expressed as ISO-8601.
[/vep] Add Paralogues plugin[/vep] Update dbNSFP data to 4.9c[/ga4gh/beacon/query] Beacon does not return DisGeNET scores anymore[/ga4gh/beacon/query] Beacon does not return Mastermind scores anymore[/vep] DisGeNET plugin is deprecated[/vep] Mastermind plugin is deprecated[/ga4gh/beacon/query] Update output format[overlap/translation/:id] Use protein feature description if no InterPro xref exists[/vep] Add VEP plugins REVEL and ClinPred[/vep] Add LOEUF plugin to VEP REST[/vep] Update dbNSFP data to 4.7c[/vep/] and [variation/] endpoints have additional gencode_primary flag"GET regulatory/species/:species/id/:id:" removed"GET regulatory/species/:species/epigenome:" removed"GET regulatory/species/:species/microarray/:microarray/vendor/:vendor:" removed"GET regulatory/species/:species/microarray:" removed"GET regulatory/species/:species/microarray/:microarray/probe/:probe:" removed"GET regulatory/species/:species/microarray/:microarray/probe_set/:probe_set:" removed"GET overlap/region/:species/:region:" updated (other_regulatory and array_probe removed as possible feature types)"GET overlap/id/:id:" update (other_regulatory and array_probe removed as possible feature types)[/variation/:species/id] Return structural variants by their ID[/variation/:species] Return structural variants by their ID[/vep/:species/id] Return structural variants by their ID[/vep/:species] Return structural variants by their ID[/vep/:species/hgvs/] New plugin option added: DosageSensitivity[/vep/:species/id/] New plugin option added: DosageSensitivity[/vep/:species/region/] New plugin option added: DosageSensitivity[/vep] Added AlphaMissense plugin[/vep] Update README URL for dbNSFP 4.5c[/vep/:species/hgvs/] New option values allowed for: CADD[/vep/:species/id/] New option values allowed for: CADD[/vep/:species/region/] New option values allowed for: CADD"GET cafe/genetree/member/id/:id""GET genetree/member/id/:id""GET homology/id/:id"[/cafe/genetree/member/id/:id] is deprecated and replaced by [/cafe/genetree/member/id/:species/:id][/genetree/member/id/:id] is deprecated and replaced by [/genetree/member/id/:species/:id][/homology/id/:id] is deprecated and replaced by [/homology/id/:species/:id][/vep] Documented OpenTargets plugin[/vep] Documented MaveDB plugin[/vep] Documented Enformer plugin[/ga4gh/beacon/query] Return VEP data in Beacon output[/lookup/] Added length attribute for transcript feature[/vep] Documented MaveDB plugin[/vep] Mention ALL keyword in documentation of dbNSFP plugin for VEP[/vep] Added Geno2MP plugin[/vep] Documented use of transcript_match option for dbNSFP plugin[/ga4gh/beacon] Upgraded Beacon to version 2[/ga4gh/beacon/query] Implement the Beacon response following specifications for version 2[/vep] Documented all valid flags in VEP REST[/variant_recoder] Documented all valid flags in VR REST[/vep] Allow to output the GA4GH Variation Representation Specification (VRS) standard[/variant_recoder] Allow to output the GA4GH Variation Representation Specification (VRS) standard[/vep/:species/hgvs/] new plugin option added: UTRAnnotator[/vep/:species/id/] new plugin option added: UTRAnnotator[/vep/:species/region/] new plugin option added: UTRAnnotator[/ga4gh/beacon] Added the dataset dbSNP[/ga4gh/beacon/query] Fix bug: the response includes the dataset dbSNP if the query includes the dataset response[/vep/:species/hgvs/] new plugin option added: NMD[/vep/:species/id/] new plugin option added: NMD[/vep/:species/region/] new plugin option added: NMD[/overlap] and [/overlap/region] Removed all references to peak type value for the Feature parameter[/vep/:species/hgvs/] New plugin option added: mutfunc. Plugin option removed: SpliceRegion[/vep/:species/id/] New plugin option added: mutfunc. Plugin option removed: SpliceRegion[/vep/:species/region/] New plugin option added: mutfunc. Plugin option removed: SpliceRegion[/family] Deprecated and removed the gene family endpoint[/vep/:species/hgvs/] New plugin options added: IntAct, EVE, and GO. Plugin option available: AncestralAllele[/vep/:species/id/] New plugin options added: IntAct, EVE, and GO. Plugin option available: AncestralAllele[/vep/:species/region/] New plugin options added: IntAct, EVE, and GO. Plugin option available: AncestralAllele[vep/:species/hgvs/:hgvs_notation] New plugin option added to select SpliceAI annotation scores from Ensembl MANE transcripts (SNV only)[vep/:species/id/:id] New plugin option added to select SpliceAI annotation scores from Ensembl MANE transcripts (SNV only)[vep/:species/region/:region/:allele/] New plugin option added to select SpliceAI annotation scores from Ensembl MANE transcripts (SNV only)[variant_recoder/:species/:id] Has the option to return VCF and variation synonyms[/lookup] and [/overlap] Added the canonical_transcript attribute to gene object, to provide the stable ID of the canonical transcript for that gene[/lookup] Added MANE object. Available only with the expand=1 and mane=1 option[/overlap] Added MANE object. Available with the feature=mane option[eqtl/] eQTL endpoints have been removed and replaced by the new eQTL catalogue API at https://www.ebi.ac.uk/eqtl/[/overlap] Added is_canonical attribute for transcript feature, for consistency with the lookup endpoint[/lookup] Added version attribute for translation feature in full format (already available in condensed format)[info/assembly/:species] "base_pairs" removed from response. Use "golden_path" instead.[/vep/:species/hgvs/] SpliceAI and DisGeNET options return data in key-value pair structures rather than concatenated strings of results[/vep/:species/id/] SpliceAI and DisGeNET options return data in key-value pair structures rather than concatenated strings of results[/vep/:species/region/] SpliceAI and DisGeNET options return data in key-value pair structures rather than concatenated strings of results[/vep/:species/hgvs/] new plugin option added: Mastermind[/vep/:species/id/] new plugin option added: Mastermind[/vep/:species/region/] new plugin option added: Mastermind[variant_recorder/:species/:id] Identifiers are now reported separately for each alternative allele of the input variant[/vep/:species/hgvs/] new plugin option added: DisGeNet[/vep/:species/id/] new plugin option added: DisGeNet[/vep/:species/region/] new plugin option added: DisGeNet[/vep/*] VEP endpoints updated to contain transcription_factors key for motif_feature_consequences[/phenotype/gene/:species/:gene] New options added: trait, tumour, non_specified[/phenotype/region/:species/:gene] New options added: trait, tumour, non_specified[/alignment/region/:species/:region] Method 'EPO_LOW_COVERAGE' replaced by 'EPO_EXTENDED'[variation/:species/:id]: The ancestral_allele field is now reported in each location hash of the mappings array[/vep]: Added the flags --shift_3prime and --shift_genomic to allow for the 3' shifting of insertions and deletions in repetitive regions before consequence calculation[/vep/:species/hgvs/] New plugin option added: SpliceAI[/vep/:species/id/] New plugin option added: SpliceAI[/vep/:species/region/] New plugin option added: SpliceAI[/info/variation/consequence_types]: Added option to include the consequence ranking for the sequence ontology terms[/vep/:species/hgvs/]: new options: CADD, mane, vcf_string, transcript_version, SpliceRegion, LoF[/vep/:species/id/]: new options: CADD, mane, vcf_string, transcript_version, SpliceRegion, LoF[/vep/:species/region/]: new options: CADD, mane, vcf_string, transcript_version, SpliceRegion, LoF[/ld/:species/region]: corrected maximum region size in documentation[/ga4gh/beacon/query]: Add support to structural variants with new fields variantType and start (optional in case of sv); changed message error display[/variant_recorder] documentation updates[regulatory/species/:species/epigenome] will return the following fields: [description, short_name, efo_accession, encode_accession, epirr_accession, full_name, name, search_terms][info] endpoints now available for vertebrate species[variant_recoder/] Also retrieve a SPDI for a given variant identifier, HGVS or SPDI notation.[species/:species/binding_matrix/:binding_matrix_stable_id/] 'max_element' key has been replaced by 'max_position_sum' in order to fix a scaling issue of the binding matrix widget[overlap/id/:id] and [overlap/region/:species/:region] Motif features will now contain a list of all the associated Transcription Factor complexescomparative genomics endpoints accept any compara database across all divisions (vertebrates, plants, fungi, metazoa, protists, bacteria, pan_homology)[alignment/region] returns undef when none of the display species is found[/stats] Display basic server statistics[/variation/:species/:id?pops=1] for population allele frequencies with no allele count, the allele_count property is not returned instead of incorrectly returning 0[/vep/:species] remove documentation of CSN option due to relevant plug-in having been removed[biotypes/name], [biotypes/groups]. These can be used for example to find all coding biotypes, or to learn more about a particular biotype[/species/:species/binding_matrix/:binding_matrix_stable_id] to retrieve binding matrices of a species[info/variation/population] REST endpoint to allow retrieval of individual names and any genders for a given population[/info/biotypes/groups] endpoint to retrieve list of available biotype groups[/info/biotypes/groups/:group/:object_type] endpoint to retrieve the properties of biotypes within provided group (and object_type)[/info/biotypes/name/:name/:object_type] endpoint to retrieve the properties of biotypes with provided name (and object_type)[/vep/:species/*] Created a frequency entry in the colocated variants entry and removed all *_maf and *_allele entries which previously reported allele frequencies. Allele frequencies are now stored in the frequency entry for a colocated variant. Allele frequencies are now reported for each alternative allele of the input variant. Allele frequencies if available are reported for the following populations: 1000 Genomes Project: afr, amr, asn, eas, eur, sas; ESP: aa, ea; gnomAD: gnomad_afr, gnomad_amr, gnomad_asj, gnomad_eas, gnomad_fin, gnomad_nfe, gnomad_oth, gnomad_sas[/variation] added genotyping_chips option to the variation endpoint[/family] the output of the family endpoint changed[/phenotype/gene/:species/:gene] New endpoint to return phenotype annotations for a given gene[/overlap/id] Removed feature type chipseq and added peak and other_regulatory as allowed feature types[/variant_recorder] Retrieve all known IDs for a given variant identifier or HGVS notation[/variation/pmid] and [/variation/pmcid] Retrieve variants by publication[/assembly/*] Include information about region synonyms[/sequence] Include initial input in output[ga4gh/beacon/*] New Global Alliance beacon implementation[info/variation/consequence_types] New info endpoint to report all variant consequence types in use by variation endpoints[phenotype/*] Phenotype descriptions now emitted in alphabetical order. Also seen in [variation/:species][variation/:species/:id] Variation endpoint now optionally returning ontology accessions[overlap/*] Stop returning errors when there is no variation data for a given request with a variation feature typeGTEx data updated to v6[/cafe/genetree] endpoints, to retrieve information about cafe trees[/family] endpoints, to retrieve information about gene families[/phenotype] endpoints, to retrieve phenotype associations overlapping a defined region[/regulatory/species/:species/epigenome] endpoint which returns information about all epigenomes available for a given species[/regulatory/species/:species/microarray] endpoint to retrieve information about all microarrays available for a given species[/regulatory/species/:species/microarray/:microarray] endpoints for more information on specific microarrays and probes within the microarray[/ga4gh]/ endpoints updated to latest version[/vep] endpointsattrib parameter for [/ld] endpoints, returns more information about the variationpopulation_name is now a required parameter for the [/ld] endpoints[/regulatory/species/:species/:id] to [/regulatory/species/:species/id/:id]user parameters in POST bodyinclude_original_region option added to [/map] endpoints[/info/species] endpoint, including hide_strain_info and strain_collection options/alignment endpointphenotypes option added to [/lookup] endpoints[/phenotype] endpoints providing phenotype annotation for genomic features[/VEP] tool[/ld/:species/region/] to compute LD values between all pairs of variants in a defined region[/transcript_haplotypes] to compute observed transcript haplotype sequences based on phased genotype data[/info/external_dbs/] now allows restricting the list of external database entries to a specified species[/sequence/id] endpoint now allows start and end parameters allowing trimming of returned sequence[info/variation/populations] list of populations for a given species[/lookup] now includes version for stable ids[/lookup] endpoint when using the expand option[/overlap] endpoint now includes gene_id, transcript_id, protein_id, exon_id, havana_gene, havana_transcript and havana_version where available[/overlap] endpoint can now retrieve band information[/info/assembly] endpoint[/variation] endpoint[/overlap] endpoint does not include failed variants[/vep] now includes new attribute "phenotype_or_disease"[/variation] endpoint now has access to additional genotype data for 1000 Genomes phase 3, as well as NextGen cow.[/vep] [/variation] endpoints now return populated fields only. No empty elements.[/ga4gh] fix for paging of results.[/variation] endpoint[/overlap] endpoint[/vep] endpoint properly prioritises user parameters over defaults[/sequence] endpoints[/hgvs] to retrieve consequence data based on a HGVS notationpopulation_genotype option added to [/variation] endpointfailed_variation field added to [/variation] endpointssegmentation, motif, chipseq, array_probe and feature_type options added to [/overlap] endpointAccept supported for POST endpoints, to specify the output format of your choiceorthoXML format added for [/homology] endpointscoordinate_system field changed to coord_system in [/info/assembly_info] endpoint[/regulatory] to retrieve data from the regulatory build[/lookup] endpointsis_canonical for Transcripts and length for Translations fields added to [/lookup] endpointstaxon_id field added to [/homology] endpointsParent field added to [/overlap/translation] endpoints to retrieve corresponding Transcriptversion for stable_id field added to [/overlap] endpointsassembly_name field has been added to most endpoints, including [/vep], [/lookup], [/map], [/variation][/vep] output has been changed to be more json compliant and hierarchicA transition from beta to a more stable interface for users, better documentation and more functionality. More features will appear over time, but these will not interfere with the existing interface wherever possible.
[/vep/:species/id/], [/vep/:species/region/]. The VEP endpoints have had their URLs altered, and the existing ID and region endpoints now accept POST messages containing many variants. Regions can be submitted in the formats supported by the VEP (vcf, hgvs, pileup, ensembl, and vep).[/archive/id/]. The archive endpoint now supports lists of IDs in POST messages.[/variation] endpoint that retrieves variants linked to a gene or transcript[/genetree/*] endpoints support JSON response format[/feature/*] endpoints renamed to [/overlap/] to more closely represent their function[/overlap/*] endpoints now support BED response format[/sequence/*] endpoints now report sequence with contextual soft-masking for features through the mask_feature option. This allows the finding of feature boundaries in raw sequence. IDs of type cds mask the UTRs, and IDs of type gene mask introns.[/ontology/descendents] changed to [/ontology/descendants][/overlap/*] endpoints[/assembly/info] renamed to [/info/assembly] to match convention[/genetree/*] endpoints no longer supporting phyloxml_aligned and phyloxml_sequence parameters. These have been replaced with aligned and sequence.[/location] endpoints have been replaced by [/overlap][/feature/] Trim features from output which overlap 5' or 3' optionally[/alignment/region/] replaces [/alignment/block/region/] and [/alignment/slice/region/][/feature] BED output is very slow for transcripts[/feature] BED output; thick and thin ends are incorrect for reverse strand transcriptsRetry-After header once limits have been hit[/info/species] to report common names of species and taxon ids[/lookup/:species/:symbol] Look up the location of an object based on a symbol[/taxonomy/name] Allow for searching of Taxonomy nodes by any linked namecontent-type back as text/plain[/homology] throws an exception when you ask for orthologues of the species the gene is from[/xrefs/symbol/:species/:symbol] does not respond to object type filtering[/xrefs] fails to report linkage types for GO xrefs[/xrefs] fails to report linkage types for ontology xrefs[/homology/id] and [/homology/symbol] failed when querying for the same species as the member[/lookup/id] and [/xrefs/symbol] were using the parameter object rather than object_type[/homology] endpoints would accept only one instance of target_taxon and target_species. We now allow multiples as intended[/feature/id] Querying for features using a negative stranded feature reversed the strand of the retrieved objectRetry-After header once limits have been hit[/assembly/info] should return those Slices which are part of the karyotype[/feature/translation/:id] Support the retrieval of splice sites with respect from a translation[/feature/translation] Improved translation feature support for GFF3[/info/analysis] Support retrieval of analysis logic names[/info/analysis] to provide logic names available[/info/biotype] Support for listing available biotypes[/info/data] has been sped up for Ensembl Genomes servers (Ensembl Bacteria)[/info/external_db] Support retrieval of external dbs[/info/external_dbs] Support the retrieval of external dbs[/lookup/id] Provide more information for a lookup ID[/info/biotypes] Support retrieval of biotypes from the rest api[/compara/homology] throws an exception when requesting ENSEMBL_PROJECTION ortholog alignmnets[/feature/id] does not work for regulatory regions[/feature/id] is failing as it thinks species is a HASH ref[/genetree/symbol] and [/feature/translation] modified to default object type[/ontology/descendents/:id] Using the zero_distance parameter destroys any output[/ontology/id/:id] Giving a bogus ontology ID causes a stack trace[/info/species] allows you to specify a division to limit the data by[/homology/id] and [/homology/symbol] have improved error reporting when IDs and symbols cannot be found##Bugfixes:
[/vep] could not find a region due to changes in the backing Lookup object[/feature/id] allows for the querying of features overlapping a stable ID[/genetree/member/id] allows for the querying of a GeneTree by one of its member's stable ID[/genetree/member/symbol] allows for the querying of a GeneTree by one of its member's symbols (its name e.g. BRAF)[/taxonomy/] provides methods for querying the Ensembl taxonomy database. This is a mirror of NCBI's taxonomy.[/ontology/] provides methods for querying the Ensembl ontology database[/lookup/id] replaces [/lookup] but the old endpoint remains active. This endpoint now supports genomic location reporting of features when output format is set to full. Please use the new endpoint.Model::Registry supports use of Ensembl Genomes' Bio::EnsEMBL::LookUp object to help loading bacteria datasetsPlack::Middleware::CrossOrigin[/species/info] now supports the vast numbers Ensembl Bacteria brings into the registryBio::EnsEMBL::LookUp configuration attributesController::Taxonomy allows for database name configurationController::Ontology allows for database name configurationapplication/x-sereal is required and extension support is .serealapplication/x-msgpack is required and extension support is .msgpackModel::Controller::[/feature] CDS no longer report a protein as an exon's ID since ID should be unique in a file. Instead this is available via the protein_id attribute[/homology] now supports the retrieval of CDNA sequences[/feature] had incorrect documentation WRT features available[/sequence/region] had not been recoded for our multiple sequence changes resulting in a broken service[/vep] was attempting to multiple intron_number and exon_number to avoid stringification of numerics; these two fields are not numeric[/feature] new endpoint for retrieval of features by a genomic location[/sequence] now responds to Content-type text/plain with an unformatted raw String of sequencePlack::Middleware::Throttle is an optional install; custom extensions available with this checkout. Brings rate limiting to the REST API service[/sequence] supports multiple sequences from a single identifier e.g. proteins from a gene identifier[/genetree] now supports CDNA sequence in PhyloXML output[/vep] alleles now an array with allele_string explicit instead of as key.[/info/species] reports the division of a species; Ensembl Genomes extensiontext/x-fasta, text-x-gff3, text/x-seqxml+xml and text/x-phyloxml+xml.[/genetree] has had NHX format retired in favor of PhyloXML[/map] Translate coordinates for transcript/translation to genomic now reports the sequence region name[/assembly/info/human] fixedGL1923.1 properly[/genetree] parameter nh_format has no effect on the newick output<Compara> configuration option; new code introduced to select the best compara available based upon species.divisionYou can’t perform that action at this time.
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