Change log

Matthew Laird edited this page Aug 3, 2018 · 32 revisions

Ensembl REST Server Change Log

Please note all dates are expressed as ISO-8601.

8.0 - 2018-09

  • Support for gnomAD data in Variation endpoints
  • Reconciling of allele frequencies from VEP endpoints to match downloadable VEP tool. This is a breaking change, of the abbreviation "maf" being replaced with "af"
  • Phenotype endpoints now report ontology terms of phenotypes
  • Fix in gene tree and alignment endpoints to no longer report a zero on the root nodes
  • Enrichment of family endpoint has changed the output format
  • New genotyping_chips option in variation endpoint
  • New endpoints [biotypes/name], [biotypes/groups]. These can be used for example to find all coding biotypes, or to learn more about a particular biotype
  • [info/variation/population] REST endpoint to allow retrieval of individual names and any genders for a given population
  • Phenotype endpoints now return MIM ids if possible, optionally Pubmed IDs, review status and submitter names

7.0 - 2018-06

New features

  • [/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)

Updated endpoints

  • [/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 followong 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

6.3 - 2018-04

  • [/phenotype/gene/:species/:gene] New endpoint to return phenotype annotations for a given gene
  • Added ambiguity flag to VEP endpoints

6.2 - 2017-12-13

  • [/overlap/id] Removed feature type chipseq and added peak and other_regulatory as allowed feature types
  • Endpoint examples in R now added

6.1 - 2017-08-22

New features

  • [/variant_recorder] Retrieve all known IDs for a given variant identifier or HGVS notation
  • [/variation/pmid] and [/variation/pmcid] Retrieve variants by publication

Updated endpoints

  • [/assembly/*] Include information about region synonyms
  • [/sequence] Include initial input in output

6.0 - 2017-05-30

New features

  • [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

Updated endpoints

  • [phenotype/*] Phenotype descriptions now emitted in alphabetical order. Also seen in [variation/:species]
  • [variation/:species/:id] Variation endpoint now optionally returning ontology accessions

Bugfixes

  • [overlap/*] Stop returning errors when there is no variation data for a given request with a variation feature type
  • Updated default server properties for new installations

5.0 - 2017-03-28

New features

  • GTEx 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

Updated endpoints

  • [/ga4gh]/ endpoints updated to latest version
  • Enable more flags in [/vep] endpoints
  • New attrib parameter for [/ld] endpoints, returns more information about the variation
  • population_name is now a required parameter for the [/ld] endpoints
  • Changed [/regulatory/species/:species/:id] to [/regulatory/species/:species/id/:id]

Bug fixes

  • Proper handling of user parameters in POST body

4.8 - 2016-12-06

  • include_original_region option added to [/map] endpoints
  • Strain information added to [/info/species] endpoint, including hide_strain_info and strain_collection options
  • The new 18-murinae whole-genome Cactus alignment can be retrieved with the /alignment endpoint
  • phenotypes option added to [/lookup] endpoints
  • New [/phenotype] endpoints providing phenotype annotation for genomic features
  • A new version of the [/VEP] tool

4.7 - 2016-10-03

  • VEP dbNSFP data updated to 3.2a
  • New VEP endpoint supporting POST vep/:species/hgvs

4.6 - 2016-07-18

  • New eQTL endpoint providing GTEx V6 gene/cis-variant correlations in 44 human tissues. Searchable by both gene and variant.
  • GA4GH endpoints updated to alpha version v0.6.0a4
  • VEP endpoints now have additional RefSeq and "merged" caches available

Fixes

  • Reduced search space in Linkage Disequilibrium (LD) endpoint, to maintain quality of service
  • LD endpoint returns additional data
  • Performance improvements to Compara endpoints

4.5 - 2016-03-09

  • New Regulation endpoint [/ld/:species/region/] to compute LD values between all pairs of variants in a defined region
  • New variation endpoint [/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
  • GA4GH endpoints updated to version 0.6.0

4.4 - 2015-12-08

New features

  • [/sequence/id] endpoint now allows start and end parameters allowing trimming of returned sequence
  • New Information endpoint [info/variation/populations] list of populations for a given species

4.3 - 2015-07-15

New features

  • [/lookup] now includes version for stable ids
  • UTR features can be retrieved from the [/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
  • is_circular attribute added to the [/info/assembly] endpoint
  • minor_allele attribute added to the [/variation] endpoint

Bug fixes

  • the [/overlap] endpoint does not include failed variants

4.2 - 2015-05-21

New features

  • [/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.

Bug fixes

  • [/vep] [/variation] endpoints now return populated fields only. No empty elements.
  • [/ga4gh] fix for paging of results.

4.1 - 2015-03-12

New features

  • Global Alliance endpoints merged onto the same server as Ensembl endpoints. These will no longer be hosted separately.
  • POST support for [/variation] endpoint
  • More efficient [/overlap] endpoint

Bug fixes

  • [/vep] endpoint properly prioritises user parameters over defaults

4.0 - 2014-12-03

New features

  • POST support added for [/sequence] endpoints
  • New VEP endpoint [/hgvs] to retrieve consequence data based on a HGVS notation
  • population_genotype option added to [/variation] endpoint
  • failed_variation field added to [/variation] endpoints
  • segmentation, motif, chipseq, array_probe and feature_type options added to [/overlap] endpoint
  • Accept supported for POST endpoints, to specify the output format of your choice
  • orthoXML format added for [/homology] endpoints
  • coordinate_system field changed to coord_system in [/info/assembly_info] endpoint

3.1.0 - 2014-10-02

New Features:

  • New Regulatory endpoint [/regulatory] to retrieve data from the regulatory build
  • POST support added for [/lookup] endpoints
  • is_canonical for Transcripts and length for Translations fields added to [/lookup] endpoints
  • taxon_id field added to [/homology] endpoints
  • Parent field added to [/overlap/translation] endpoints to retrieve corresponding Transcript
  • version for stable_id field added to [/overlap] endpoints

3.0.1 - 2014-08-22

New Features:

  • An assembly_name field has been added to most endpoints, including [/vep], [/lookup], [/map], [/variation]

Bugfixes

  • Add line break for sequences
  • Better error handling in plain type

3.0.0 - 2014-07-08

New Features:

  • [/vep] output has been changed to be more json compliant and hierarchic

2.0.0 - 2014-06-26

A 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.

New Features:

  • New POST endpoints. POST messages allow the user to potentially submit huge quantities of requests, so please be kind, observe any rate and message size limits, and make your clients tolerant to timeouts and errors.
    • [/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.
  • HTTPS support for clients working within a secure environment
  • The rate limiter is set to 15 requests per second (an increase from 3)

Bugfixes:

  • Spelling of [/ontology/descendents] changed to [/ontology/descendants]
  • Documentation overhaul to better explain endpoints and parameters
  • Regulatory features appear correctly from [/overlap/*] endpoints
  • Numerous tweaks to error handling and documentation
  • [/assembly/info] renamed to [/info/assembly] to match convention

Retirements:

  • MessagePack and Sereal formats were receiving little use and have been retired to decrease maintenance burden
  • [/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]

Deployment issues:

  • New versions of Moose, Catalyst and Catalyst::Action::REST are causing misbehaviour with the server. Please observe the library versions required in the installation makefile until we find a way to fix this conflict.

1.6.0 - 2014-02-26

New Features:

  • [/feature/] Trim features from output which overlap 5' or 3' optionally
  • [/alignment/region/] replaces [/alignment/block/region/] and [/alignment/slice/region/]

Bugfixes:

  • The example for multiple alignments is wrong
  • XS assert_ref fails with REST feature endpoint
  • [/feature] BED output is very slow for transcripts
  • [/feature] BED output; thick and thin ends are incorrect for reverse strand transcripts

1.5.1 - 2013-12-04

Bugfixes:

  • Removed deprecated methods from Compara

1.5.0 - 2013-12-04

New Features:

  • Build a better rate limiter
  • Enable compression on REST site
  • Ensure rate limiter reports the time scale over which rate limiting occurs
  • Faster GeneTree serlialisation; JSON now supported
  • Rate limiter responds with a Retry-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 name

Bugfixes:

  • Detect content in REST does not understand Accepts
  • GFF3 for cds features invalid, duplicate ids for simple features
  • Serialisations choose to send the content-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

1.4.4 - 2013-11-07

Bugfixes

  • [/xrefs] fails to report linkage types for ontology xrefs
  • [/homology/id] and [/homology/symbol] failed when querying for the same species as the member

1.4.3 - 2013-11-05

Bugfixes:

  • [/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

1.4.2 - 2013-09-23

Bugfixes:

  • [/feature/id] Querying for features using a negative stranded feature reversed the strand of the retrieved object

1.4.1 - 2013-09-09

Bugfixes:

  • Lookup with a non-indexed stable identifiers in databases other than core failed

1.4.0 - 2013-09-03

New Features:

  • Improved error page when a user goes to an unknown documentation page
  • Rate limiter responds with a Retry-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

Bugfixes:

  • REST GFF CDS Line is incorrect. ID can repeat in a single GFF file
  • [/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

1.3.2 - 2013-04-16

New Features:

  • [/info/species] allows you to specify a division to limit the data by

Bugfixes:

  • [/homology/id] and [/homology/symbol] have improved error reporting when IDs and symbols cannot be found

1.3.1 - 2013-04-15

##Bugfixes:

  • [/vep] could not find a region due to changes in the backing Lookup object

1.3.0 - 2013-04-09

New Features:

  • [/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 datasets
  • All location based services no longer support underscores as a numeric separator. All now support UCSC names for sequence regions
  • Support for CrossOrigin resource sharing via Plack::Middleware::CrossOrigin

Configuration:

  • [/species/info] now supports the vast numbers Ensembl Bacteria brings into the registry
  • All models if they need access to the Catalyst context object implement methods to access this without explicit pass throughs. Affects all Models apart from Registry

Bugfixes:

  • Model::Registry has Bio::EnsEMBL::LookUp configuration attributes
  • Controller::Taxonomy allows for database name configuration
  • Controller::Ontology allows for database name configuration

1.2.0 - 2013-02-15

New Features:

  • Support for Sereal encoding format from Sereal::Encoder. MIME type application/x-sereal is required and extension support is .sereal
  • Support for MessagePack encoding format from Data::MessagePack. MIME type application/x-msgpack is required and extension support is .msgpack

Configuration:

  • Configuration has switched to a more Catalyst friendly method. Config is namespaced to the object which uses it and is accessible via local accessors in that object.
    • Registry and Documentation are prefixed with Model::
    • Feature and Sequence are prefixed with Controller::
    • All other configuration sections are unaffected

Bugfixes:

  • [/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

1.1.2 - 2012-10-24

Output:

  • [/homology] now supports the retrieval of CDNA sequences

Bugfixes:

  • [/feature] had incorrect documentation WRT features available

1.1.1 - 2012-10-24

Bugfixes:

  • [/sequence/region] had not been recoded for our multiple sequence changes resulting in a broken service
  • Documentation needs to internally escape characters like + for example as Catalyst does not like this
  • [/vep] was attempting to multiple intron_number and exon_number to avoid stringification of numerics; these two fields are not numeric

1.1.0 - 2012-10-23

New Features:

  • [/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 sequence
  • Plack::Middleware::Throttle is an optional install; custom extensions available with this checkout. Brings rate limiting to the REST API service
  • Using CHI to cache documentation API responses
  • Content type detection carried out using file name extensions as well as the existing mechanisms. Supported on all endpoints
  • [/sequence] supports multiple sequences from a single identifier e.g. proteins from a gene identifier
  • Online change log
  • [/genetree] now supports CDNA sequence in PhyloXML output

Output:

  • [/vep] alleles now an array with allele_string explicit instead of as key.
  • [/info/species] reports the division of a species; Ensembl Genomes extension
  • Mime types changed for many services to denote non-standard types. We now use text/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

Bugfixes:

  • 2 Y regions returned from [/assembly/info/human] fixed
  • JSON serialiser mis-encodes numerics as Strings due to MySQL DBD issues
  • Location parser method does not handle GL1923.1 properly
  • [/genetree] parameter nh_format has no effect on the newick output

Configuration:

  • Removal of <Compara> configuration option; new code introduced to select the best compara available based upon species.division
  • Documentation supports variable replacement for easier configuration by third parties
  • CHI cache support in configuration; see CHI's POD and our production configuration about how you can configure it
  • URL, name and logo now configurable

1.0.0 - 2012-09-05

  • Initial revision of REST API
  • Support for comparative genomics, cross references, ID lookup, mapping coordinates, sequences & variations
  • Information endpoints also made available
  • Documentation added for all end points
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