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Release 90

External database references update (all species)

Xrefs updates for: homo_sapiens (human), mus_musculus (mouse), rattus_norvegicus (rat), sus_scrofa (pig)

Release 89

GO terms for transcripts (all species)

GO terms have been introduced for some miRNAs. As a result, GO terms are now linked to transcripts rather than translations.

External database references update (multiple species)

Xrefs updates for: homo_sapiens (human), mus_musculus (mouse), danio_rerio (zebrafish), loxondonta africana (elephant), notamacropus eugenii (wallaby), papio anubis (olive baboon), ochotona princeps (pika), procavia capensis (hyrax), pteropus vampirus (megabat), tupaia belangeri (tree shrew), anas platyrhynchos (duck), dasypus novemcinctus (armadillo), ictidomys tricemlineatus (squirrel), gasterosteus aculeatus (stickleback)

Vega xrefs retirement (Zebrafish, Human, Mouse, Rat, Pig)

Links to Vega resources have been removed for the following species: human, mouse, rat, zebrafish, pig

Release 88

External database references update (multiple species)

Xref updates for: alpaca, dolphin, fugu, gibbon, guinea pig, human, kangaroo rat, marmoset, mouse, orangutan, panda, platyfish, rat, sloth, tarsier, tasmanian devil and xenopus.

patch_87_88_b.sql (all species)

Name column in seq_region table expanded to varchar(255)

Release 87

EBeye Dumps (all species)

Generate search indexes to be used at the EBI.

Ensembl VM Build (all species)

The Ensembl Virtual Machine applicance will be updated to version 87.

External database references update (multiple species)

Xref updates for: homo_sapiens (human), mus_musculus (mouse), danio_rerio (zebrafish), felis_catus (domestic cat), gadus_morhua (atlantic cod), poecilia_formosa (amazon molly), monodelphis_domestica (gray short-tailed opossum), bos_taurus (cattle), gorilla_gorilla (western lowland gorilla), meleagris_gallopavo (domestic turkey),equus_caballus (horse), tetraodon_nigroviridis (spotted green pufferfish), myotis_lucifugus (little brown bat)

LRG Import (all species)

Importing the latest version of Locus Reference Genomic dataset.

patch_86_87_a.sql - schema_version update (all species)

Update schema_version in meta table to 87.

patch_86_87_a.sql - schema_version update in ontology db (all species)

Update schema_version in meta table to 87.

patch_86_87a.sql - schema_version update in production db (all species)

Update schema_version in production database to 87.

REST server upgrade (all species)

REST server updated to latest API and data

Stable ID lookup (all species)

Stable ID lookup provided for REST services.

Includes lookup for RefSeq and CCDS entries.

Other Core DB Patches (all species)

patch_86_87_b.sql
 -- Enforced meta_value in meta table to be NOT NULL

patch_86_87_c.sql
 -- DATETIME DEFAULT is set to NULL (earlier it was '0000-00-00 00:00:00')

patch_86_87_b.sql - meta_value in meta table is set to be NOT NULL (all species)

patch_86_87_b.sql
 -- Enforced meta_value in meta table to be NOT NULL
Altered table meta

patch_86_87_c.sql - DATETIME default is set to be NULL (all species)

patch_86_87_c.sql
 -- DATETIME DEFAULT is set to NULL (earlier it was '0000-00-00 00:00:00')
Altered tables (genome_statistics, analysis, exon, gene, transcript, translation, operon, operon_transcript) 

Release 86

EBeye Dumps (all species)

Generate search indexes to be used at the EBI.

Ensembl VM Build (all species)

The Ensembl Virtual Machine applicance will be updated to version 85.

External database references update (multiple species)

Xref updates for: homo_sapiens (human), mus_musculus (mouse), danio_rerio (zebrafish), erinaceus_europaeus (hedgehog), ciona_savignyi (Sea squirt), sorex_araneus (European shrew), petromyzon_marinus (sea lamprey), oryzias_latipes (Japanese medaka), taeniopygia_guttata (zebra finch), chlorocebus_sabaeus (African green monkey), anolis_carolinensis (green anole), ornithorhynchus_anatinus (platypus), otolemur_garnettii (small-eared galago), ovis_aries (sheep)

LRG Import (all species)

Importing the latest version of Locus Reference Genomic dataset.

patch_85_86_a.sql - schema_version update (all species)

Update schema_version in meta table to 86.

patch_85_86_a.sql - schema_version update in ontology db (all species)

Update schema_version in meta table to 86.

patch_85_86_a.sql - schema_version update in production db (all species)

Update schema_version in production database to 86.

REST server upgrade (all species)

REST server updated to latest API and data

Stable ID lookup (all species)

Stable ID lookup provided for REST services.

Includes lookup for RefSeq and CCDS entries.

Release 85

patch_84_85_a.sql - schema_version update (all species)

Update schema_version in meta table to 85.

patch_84_85_a.sql - schema_version update in ontology db (all species)

Update schema_version in meta table to 85.

patch_84_85_a.sql - schema_version update in production db (all species)

Update schema_version in production database to 85.

External database references update (multiple species)

Xref updates for: homo_sapiens (human), mus_musculus (mouse), rattus_norvegicus (rat) pan troglodytes (chimp), gallus_gallus (chicken), ficedula_albicollis (flycatcher), anas_platyrhynchos (duck), tupaia_belangeri (tree shrew), erinaceus_europaeus (hedgehog), pelodiscus_sinensis (chinese softshell turtle), latimeria_chalumnae (coelacanth), oryctolagus_cuniculus (rabbit), echinops_telfairi (lesser hedgehog tenrec), ictidomys_tridecemlineatus (squirrel), gasterosteus_aculeatus (stickleback), ciona_savignyi (sea squirt)

Stable ID lookup (all species)

Stable ID lookup provided for REST services.

Includes lookup for RefSeq and CCDS entries.

LRG Import (Human)

Importing the latest version of Locus Reference Genomic dataset.

EBeye Dumps (all species)

Generate search indexes to be used at the EBI.

REST server upgrade (all species)

REST server updated to latest API and data

Ensembl VM Build (all species)

The Ensembl Virtual Machine applicance will be updated to version 85.

patch_84_85_b.sql - duplicate key (all species)

Remove duplicate key in genome_statistics table.

patch_84_85_b.sql - confident releationships in ontology db (all species)

Add a column in table closure to flag if it's a confident relationship (is_a, part_of, occurs_in) when calculating closure.

patch_84_85_b.sql - add synonym dbxref in ontology db (all species)

Add a column to table synonym to hold the dbxref.

New API methods (all species)

protein_feature_adaptor->fetch_all and protein_feature_adaptor->fetch_all_by_logic_name methods

exon->is_coding method

intron->rank method

slice->get_all_Transcripts_by_type and slice->get_all_Transcript_by_source methods

Database schema patches (all species)

The Ensembl Regulation Database Schema has received a number of improvements for the Ensembl Release 85. Here is the complete list:

patch_84_85_a.sql - schema version
Update schema_version in meta table to 85


patch_84_85_b.sql - rename cell_type table to epigenome
The cell_type table may contain entries that are not specific to a single cell type


patch_84_85_c.sql - new columns to the epigenome table
Modify existing or add new columns to the epigenome table


patch_84_85_d.sql - add columns to experiment table
Add new columns to the experiment table in order to facilitate ERSA control grouping


patch_84_85_e.sql - add/modify columns in input_subset table
Add/modify columns in input_subset table


patch_84_85_f.sql - drop replicate column from result_set table
There is no need for a replicate column in the result_set table.


patch_84_85_g.sql - update dbentry related tables.
Updates to catch up with developments from the core schema and allow xrefs to be stored for epigenomes.


patch_84_85_h.sql - Store file types.
Store file types along with the files.


patch_84_85_i.sql - Normalise regulatory feature table: Create a non redundant version of the regulatory features
Also remove column "projected".


patch_84_85_j.sql - Normalise regulatory feature table
Create a linking table between regulatory features and feature sets.


patch_84_85_k.sql - Normalise regulatory feature table
Link up the new non redundant regulatory features. The new regulatory_feature_ids are set. The connection is made using the stable ids.


patch_84_85_l.sql - Normalise regulatory feature table
Link up the regulatory attributes with the linking table.


patch_84_85_m.sql - Normalise regulatory feature table
Clean up temporary columns and tables.


patch_84_85_n.sql - Make activity an enum.


patch_84_85_o.sql - Delete all MultiCell regulatory features feature set entries.


patch_84_85_p.sql - Delete MultiCell feature_set and epigenome


patch_84_85_q.sql - Rename table regulatory_attribute to regulatory_evidence


patch_84_85_r.sql - Drop unused empty tables
These tables are empty and of no use. No need to keep them

patch_84_85_s.sql - modify 'table_name' column in result_set_input table
Remove enum values from 'table_name' column that are of no use

patch_84_85_t.sql - Drop table regbuild_string

patch_84_85_u.sql - Remove regulatory build entries from feature_set table, relink everything else.

patch_84_85_v.sql - Move meta entries regarding regulatory build to the regulatory_build table

patch_84_85_w.sql - Extend the name length in the input_subset table

patch_84_85_x.sql - Remove unused columns in the experiment table
Remove primary_design_type, description, mage_xml_id, display_url

patch_84_85_y.sql - Table for storing epigenomes used in the regulatory build

patch_84_85_z.sql - Move segmentation entries from result_set table into the new segmentation_file table.

patch_84_85_za.sql - Move entries provided by external sources from the result_set table into the new external_feature_file table.

patch_84_85_zb.sql - Bugfix, the primary key was wrongly named.

API changes, deprecation list (all species)

This list contains all methods, modules and scripts deprecated in the Ensembl Funcgen API. A method is deprecated when it is not functional any more (schema/data change) or has been replaced by a better one. Backwards compatibility is provided whenever possible. When a method is deprecated, a deprecation warning is thrown whenever the method is used. The warning also contains instructions on replacing the deprecated method and when it will be removed. A year after deprecation (4 Ensembl releases), the method is removed from the API.

### Deprecated in Ensembl Release 85, to be removed in Ensembl Release 89 ###
 - Bio::EnsEMBL::Funcgen::**ResultSet**::*replicate()*
 - Bio::Ensembl::Funcgen::DBSQL::**CellTypeAdaptor**
 - Bio::Ensembl::Funcgen::**CellType**
 - Bio::EnsEMBL::Funcgen::**DataSet**::*cell_type()*
 - Bio::EnsEMBL::Funcgen::**Experiment**::*cell_type()*
 - Bio::EnsEMBL::Funcgen::**Importer**::*cell_type()*
 - Bio::EnsEMBL::Funcgen::**SetFeature**::*cell_type()*
 - Bio::EnsEMBL::Funcgen::**Set**::*cell_type()*
 - Bio::EnsEMBL::Funcgen::**Epigenome**::*efo_id()*
 - Bio::EnsEMBL::Funcgen::**Experiment**::*primary_design_type()*
 - Bio::EnsEMBL::Funcgen::**Experiment**::*description()*
 - Bio::EnsEMBL::Funcgen::**Experiment**::*mage_xml()*
 - Bio::EnsEMBL::Funcgen::**Experiment**::*mage_xml_id()*
 - Bio::EnsEMBL::Funcgen::**RegulatoryFeature**::*cell_type_count()*
 - Bio::EnsEMBL::Funcgen::DBSQL::**ExperimentAdaptor**::*fetch_all_by_CellType()*
 - Bio::EnsEMBL::Funcgen::DBSQL::**MotifFeatureAdaptor**::*fetch_all_by_Slice_CellType()*
 - Bio::EnsEMBL::Funcgen::DBSQL::**SetAdaptor**::*fetch_all_by_CellType()*
 - Bio::EnsEMBL::Funcgen::**RegulatoryFeature**::*get_focus_attributes*
 - Bio::EnsEMBL::Funcgen::**RegulatoryFeature**::*get_nonfocus_attributes*
 - Bio::EnsEMBL::Funcgen::**RegulatoryFeature**::*is_unique_to_FeatureSets*
 - Bio::EnsEMBL::Funcgen::**RegulatoryFeature**::*get_other_RegulatoryFeatures*
 - Bio::EnsEMBL::Funcgen::**RegulatoryFeatureAdaptor**::*fetch_all_by_stable_ID*

### Removed in Ensembl Release 85 ### - Bio::Ensembl::Funcgen::**Experiment**::*date()* - Bio::Ensembl::Funcgen::**ResultSet**::*get_replicate_set_by_chip_channel_id()* - Bio::Ensembl::Funcgen::DBSQL::**BaseAdaptor**::*list_dbIDs()* - Bio::Ensembl::Funcgen::DBSQL::**BaseAdaptor**::*_constrain_status()* - Bio::Ensembl::Funcgen::DBSQL::**BaseAdaptor**::*fetch_all_by_status()* - Bio::Ensembl::Funcgen::DBSQL::**DBEntryAdaptor**::*list_regulatory_feature_ids_by_extid()* - Bio::Ensembl::Funcgen::DBSQL::**DBEntryAdaptor**::*list_probeset_ids_by_extid()* - Bio::Ensembl::Funcgen::DBSQL::**DBEntryAdaptor**::*list_feature_type_ids_by_extid()* - Bio::Ensembl::Funcgen::DBSQL::**DBEntryAdaptor**::*list_external_feature_ids_by_extid()* - Bio::Ensembl::Funcgen::DBSQL::**DBEntryAdaptor**::*list_annotated_feature_ids_by_extid()* - Bio::Ensembl::Funcgen::DBSQL::**DBEntryAdaptor**::*list_probe_ids_by_extid()* - Bio::Ensembl::Funcgen::DBSQL::**FeatureSetAdaptor**::*fetch_all_by_type()* - Bio::Ensembl::Funcgen::DBSQL::**InputSubsetAdaptor**::*fetch_by_name_and_experiment()* - Bio::Ensembl::Funcgen::DBSQL::**ProbeFeatureAdaptor**::*fetch_all_by_probeset()* - Bio::Ensembl::Funcgen::DBSQL::**ResultFeatureAdaptor**::*fetch_all()* - Bio::Ensembl::Funcgen::DBSQL::**ResultFeatureAdaptor**::*fetch_by_dbID()* - Bio::Ensembl::Funcgen::DBSQL::**ResultFeatureAdaptor**::*fetch_all_by_dbID_list()* - Bio::Ensembl::Funcgen::DBSQL::**ResultFeatureAdaptor**::*fetch_all_by_logic_name()* - Bio::Ensembl::Funcgen::DBSQL::**ResultFeatureAdaptor**::*_list_seq_region_ids()* - Bio::Ensembl::Funcgen::DBSQL::**ResultSetAdaptor**::*store_dbfile_data_dir()* - Bio::Ensembl::Funcgen::DBSQL::**ResultSetAdaptor**::*_fetch_dbfile_data_dir()*

Release 84

patch_83_84_a.sql - schema_version update (all species)

Update schema_version in meta table to 84.

patch_83_84_a.sql - schema_version update in production db (all species)

Update schema_version in production database to 84.

Stable ID lookup (all species)

Stable ID lookup provided for REST services

Includes lookup for RefSeq and CCDS entries

Ensembl VM Build (all species)

The Ensembl Virtual Machine applicance will be updated to version 84.

LRG Import (Human)

Importing the latest version of Locus Reference Genomic dataset.

patch_83_84_c.sql - new unique key for protein_feature (all species)

Patch to avoid duplicate protein features ending up in the database which are later caught by HCs.

patch_83_84_b.sql - xref.version default (all species)

Should default to NULL - many xrefs e.g. GO don't have an explicit version, current 0 does not make sense.

RDF dumps (all species)

RDF dumps for all species.

patch_83_84_a.sql - schema_version update in ontology db (all species)

Update schema_version in meta table to 84.

External database references update (multiple species)

Xref updates for:

mus_musculus (mouse), homo_sapiens (human), danio_rerio (zebrafish), ailuropoda_melanoleuca (panda), choloepus_hoffmanni (sloth), dasypus_novemcinctus (armadillo), dipodomys_ordii (kangaroo rat), loxodonta_africana (elephant), macropus_eugenii (wallaby), microcebus_murinus (mouse lemur), ochotona_princeps (pika), procavia_capensis (hyrax), pteropus_vampyrus (megabat), tarsius_syrichta (tarsier), tursiops_truncatus (dolphin), vicugna_pacos (alpaca)

patch_83_84_d.sql - longer synonym (all species)

Update seq_region_synonym table to allow longer synonym column

patch_83_84b.sql - division tables in production db (all species)

Division specific tables are added in the production database for compatibility with Ensembl Genomes

Feature parameter in REST /info/external_dbs (all species)

Restricts the list of external database entries to those used for a specific feature type

Release 83

Ensembl VM Build (all species)

The Ensembl Virtual Machine applicance will be updated to version 83.

LRG Import (Human)

Importing the latest version of Locus Reference Genomic dataset

patch_82_83_a.sql - schema_version update (all species)

Update schema_version in meta table to 83.

patch_82_83a.sql - schema_version update in production db (all species)

Update schema_version in production database to 83.

Stable ID lookup (all species)

Stable ID lookup provided for REST services

Includes lookup for RefSeq and CCDS entries

External database references update (multiple species)

Xrefs update for:

mus_musculus (mouse), homo_sapiens (human), rattus_norvegicus (rat), callithrix_jacchus (marmoset), pongo_abelii (orangutan), cavia_porcellus (guinea  pig), xiphophorus_maculatus (platyfish), oreochromis_niloticus (tilapia), sus_scrofa (pig), mustela_putorius_furo (ferret), nomascus_leucogenys (gibbon), lepisosteus_oculatus (Spotted gar), astyanax_mexicanus (cave fish), takifugu_rubripes (fugu), xenopus_tropicalis (xenopus), sarcophilus_harrisii  (Tasmanian devil)

Added start/end parameters for sequence endpoint (REST) (all species)

Allows to restrict a sequence to the specified start and end coordinates

RDF dump (all species)

RDF dumps for all species

Schema changes (all species)

  • New 'ExAC' evidence (column evidence_attribs) in the variation and variation_feature tables.
  • Remove the column 'validation_status' from the variation and variation_feature tables.

Release 82

Ensembl VM Build (all species)

The Ensembl Virtual Machine applicance will be updated to version 82.

External database references update (multiple species)

Xrefs update for:

mus_musculus (mouse), homo_sapiens (human), poecilia_formosa (amazon molly), monodelphis_domestica (opposum), bos_taurus (cow), macaca_mulatta (rhesus monkey), gorilla_gorilla (gorilla), equus_caballus (horse), gadus_morhua (cod), meleagris_gallopavo (turkey), felis_catus (cat), tetraodon_nigroviridis (pufferfish), myotis_lucifugus (microbat)

LRG Import (Human)

Importing the latest version of Locus Reference Genomic dataset

patch_81_82_a.sql - schema_version update (all species)

Update schema_version in meta table to 82.

patch_81_82_a.sql - schema_version update in ontology db (all species)

Update schema_version in meta table to 82.

patch_81_82a.sql - schema_version update in production db (all species)

Update schema_version in production database to 82.

Stable ID lookup (all species)

Stable ID lookup provided for REST services

Includes lookup for RefSeq and CCDS entries

patch_81_82_b.sql - xref_width (all species)

Extend column width for xref display_label and dbprimary_acc

patch_81_82_c.sql - seq_synonym_key (all species)

update unique on seq_region_synonym table to include seq_region_id

VEP plugins (REST) (all species)

VEP REST endpoints to support use of VEP plugins

Release 81

Ensembl VM Build (all species)

The Ensembl Virtual Machine applicance will be updated to version 81.

External database references update (multiple species)

Xrefs update for:

homo_sapiens (human), mus_musculus (mouse), otolemur_garnetii (mouse lemur), sorex_araneus (shrew), oryzias_latipes (medaka), pan_troglodytes (chimp), petromyzon_marinus (lamprey), taeniopygia_guttata (zebrafinch), ovis_aries (sheep), canis_familiaris (dog), ciona_intestinalis (sea squirt), anolis_carolinensis (anole lizard), chlorocebus_sabaeus (vervet monkey), ornithorhynchus_anatinus (platypus)

LRG Import (all species)

Importing the latest version of Locus Reference Genomic dataset

patch_80_81_a.sql - schema_version update (all species)

Update schema_version in meta table to 81.

patch_80_81_a.sql - schema_version update in ontology db (all species)

Update schema_version in meta table to 81.

patch_80_81a.sql - schema_version update in production db (all species)

Update schema_version in production database to 81.

Stable ID lookup (all species)

Stable ID lookup provided for REST services

Includes lookup for RefSeq and CCDS entries

UTR features in the REST API (all species)

UTR features can be retrieved using the REST API

Band information in the REST API (all species)

Band information can be retrieved via the overlap endpoint in the REST API

New UTR, CDS and ExonTranscript features (all species)

The Ensembl API supports the retrieval of UTR, CDS and ExonTranscript features

UTR features represent the non-coding exons of a transcript, CDS features represent the coding exons of a transcript

ExonTranscript features are Exons which retain the link to their parent transcript as well as their rank

Schema update: Storing sample data (all species)

We updated the way how we store populations, individuals and samples. With the updated schema we can store samples for an individual. All genotypes and read coverage data will be stored on the sample level.

New table:

  • sample

Rename tables:

  • individual_population to sample_population
  • individual_genotype_multiple_bp to sample_genotype_multiple_bp

The change is reflected in tables that store individual data. Individual_id is changed to sample_id in the following tables:

  • compressed_genotype_region
  • read_coverage
  • structural_variation_sample

Update columns in individual table: display, has_coverage and variation_set_id columns moved into the new sample table and have been deleted from the individual table.

API support for the new sample schema (all species)

We updated our API to work with the new sample schema.

Add new modules for representing, creating and storing sample objects.:

  • Sample.pm and SampleAdaptor.pm

Rename modules:

  • IndividualGenotype.pm to SampleGenotype.pm
  • IndividualGenotypeFeature.pm to SampleGenotypeFeature.pm
  • IndividualGenotypeAdaptor.pm to SampleGenotypeAdaptor.pm
  • IndividualGenotypeFeatureAdaptor.pm to SampleGenotypeFeatureAdaptor.pm

Updated variable names from individual to sample in almost all modules in the variation API. 

Updated scripts and pipelines.

Our test suite has been updated accordingly.

GFF3 dumps (all species)

Ensembl gene annotation will be provided in GFF3 files, along with the already existing GTF files

Release 80

Ensembl VM Build (all species)

The Ensembl Virtual Machine applicance will be updated to version 80.

External database references update (multiple species)

Xrefs update for:

danio_rerio (zebrafish), homo_sapiens (human), rattus_norvegicus (rat), mus_musculus, (mouse), gasterosteus_aculeatus (stickleback), latimeria_chalumnae (coealacanth), ciona_savignyi, anas_platyrhynchos (duck), tupaia_belangeri (tree shrew), erinaceus_europaeus (hedgehog), echinops_telfairi (tenrec), ictidomys_tridecemlineatus (squirrel), oryctolagus_cuniculus (rabbit), pelodiscus_sinensis (softshell turtle), ficedula_albicollis (flycatcher), papio_anubis (olive baboon)

LRG Import (Human)

Importing the latest version of Locus Reference Genomic dataset

patch_79_80_a.sql - schema_version update (all species)

Update schema_version in meta table to 80.

Stable ID lookup (all species)

Stable ID lookup provided for REST services

Includes lookup for RefSeq and CCDS entries

patch_79_80a.sql - schema_version update in production db (all species)

Update schema_version in production database to 80.

patch_79_80_a.sql - schema_version update in ontology db (all species)

Update schema_version in meta table to 80.

start_lost to replace initiator_codon_variant consequence type (all species)

We will replace the use of initiator_codon_variant with the more specific start_lost. The difference between the two is largely semantic.

The new term protein_altering_variant will be used for variants within the protein which are not better described by any of its child terms 

API: new method to get the multiple alignment of several homologues (all species)

The new method is GeneTree::get_alignment_of_homologues($ref_member)

patch_79_80_b.sql (all species)

increase length of dbprimary_acc column in xref table

patch_79_80_c.sql (all species)

increase length of synonym column in seq_region_synonym table

patch_79_80_d.sql (all species)

increase length of value column in genome_statistics table

Release 79

patch_78_79_b.sql - Support for BAMCOV (all species)

Schema support for future BAMCOV support in the web interface.

Stable ID lookup (all species)

Stable ID lookup provided for REST services

Includes lookup for RefSeq and CCDS entries

Ensembl VM Build (all species)

The Ensembl Virtual Machine applicance will be updated to version 79.

External database references update (multiple species)

Xrefs update for:

human, chicken, panda, sloth, armadillo, kangaroo rat, elephant, wallaby, pika, mouse lemur, rock hyrax, megabat, tasmanian devil, fugu, tarsier, dolphin, alpaca, xenopus

LRG Import (all species)

Importing the latest version of Locus Reference Genomic dataset

patch_78_79_a.sql - schema_version update (all species)

Update schema_version in meta table to 79.

patch_78_79_a.sql - schema_version update in ontology db (all species)

Update schema_version in meta table to 79.

patch_78_79a.sql - schema_version update in production db (all species)

Update schema_version in production database to 79.

Update to overlap/translation REST endpoint (all species)

Endpoint updated to provide only variations overlapping the protein sequence, not the whole transcript

assembly.overlapping_regions retired (all species)

assembly.overlapping_regions meta_key retired and removed from core databases

marker.priority retired (all species)

marker.priority meta_key retired and removed from core databases

Support for polyploid genomes (all species)

New methods in the Slice object to provide support for polyploid genomes

Allows to fetch slices for a given component

Synonym types in ontologies (all species)

Ontology schema updated to provide the type for synonyms

Global Alliance REST Endpoints (all species)

New Global Alliance standard REST endpoints will be available for sets of variation data

Release 78

External database references update (all species)

Xrefs update for:

human, mouse, rat, cod, turkey, cat, marmoset, guinea pig, platyfish, tetraodon, orangutan, microbat, nile tilapia, gibbon, ferret, cave fish, spotted gar.

Stable ID lookup (all species)

Stable ID lookup provided for REST services

Includes lookup for RefSeq and CCDS entries

patch_77_78_b.sql - source column size increase (all species)

New Refseq data requires a larger source column in the gene and transcript tables.

patch_77_78_a.sql - schema_version update in ontology db (all species)

Update schema_version in meta table to 78.

patch_77_78a.sql - schema_version update in production db (all species)

Update schema_version in production database to 77.

LRG Import (all species)

Importing the latest version of Locus Reference Genomic dataset

Variation API changes (all species)

  • Add a new object "Source" handling the source data used in several Variation API objects.

REST support for multiple sequences (all species)

The sequence endpoint should accept requests for multiple sequences in a POST request.

Adjust Unmapped_reason table (all species)

Change unmapped_reason_id from smallint to int to match Regulation requirements

patch_77_78_c.sql (all species)

Integrate schema changes to support Regulation requirements

Multiple assembly support for REST sequence endpoints (Human)

For human, sequence will be available for previous assemblies as well as the current one

patch_77_78_c.sql - master_unmapped_reason (all species)

master_unmapped_reason patched to match datatype with core schema.

patch_77_78_a.sql - schema_version update (all species)

Update schema_version in meta table to 78.

Ensembl VM Build (all species)

The Ensembl Virtual Machine applicance will be updated to version 78.

Release 77

LRG Import (Human)

Importing the latest version of Locus Reference Genomic dataset

Improved GeneAdaptor::fetch_nearest_Gene_by_Feature() (all species)

We are improving our code for retrieving the nearest gene to any Ensembl feature.

patch_76_77a.sql - schema_version update in production db (all species)

Update schema_version in production database to 77.

Stable ID lookup (all species)

Stable ID lookup provided for REST services

Includes lookup for RefSeq and CCDS entries

patch_76_77_a.sql - schema_version update in ontology db (all species)

Update schema_version in meta table to 77.

External database references update (all species)

Xrefs update for:

human, rat, anolis, cow, dog, ciona intestinalis, horse, chicken, gorilla, macaque, opposum, platypus, medaka, sheep, chimp, lamprey, pig, zebrafinch, shrew

patch_76_77_a.sql - schema_version update (all species)

Update schema_version in meta table to 77.

Ensembl VM Build (all species)

The Ensembl Virtual Machine applicance will be updated to version 77.

Release 76

LRG Import (Human)

Importing the latest version of Locus Reference Genomic dataset

patch_75_76a.sql - schema_version update in production db (all species)

Update schema_version in production database to 76.

Stable ID lookup (all species)

Stable ID lookup provided for REST services

Includes lookup for RefSeq and CCDS entries

patch_75_76_a.sql - schema_version update in ontology db (all species)

Update schema_version in meta table to 76.

External database references update (multiple species)

Xrefs update for:

human, mouse, lamprey, ciona savignyi, gorilla, tenrec, shrew, hedgehog, mouse lemur, squirrel, softshell turtle, flycatcher, rabbit, zebrafinch, dog, duck

patch_75_76_a.sql - schema_version update (all species)

Update schema_version in meta table to 76.

patch_75_76_b.sql - allow null karyotype (all species)

Band and stain column in karyotype table can be null

Ensembl VM Build (all species)

The Ensembl Virtual Machine applicance will be updated to version 76.

Includes a larger disk space for VEP compatibility

patch_75_76_c.sql - alternative splicing event retirement (all species)

Remove splicing event tables which are not used any more.

Retirement of splicing event related material (all species)

Match the removal of the splicing_event tables, by retiring the corresponding modules:

- Bio::EnsEMBL::DBSQL::SplicingEventAdaptor

- Bio::EnsEMBL::DBSQL::SplicingEventFeatureAdaptor

Bio::EnsEMBL::DBSQL::SplicingTranscriptPairAdaptor

- Bio::EnsEMBL::SplicingEvent

- Bio::EnsEMBL::SplicingEventFeature

- Bio::EnsEMBL::SplicingTranscriptPair

Release 75

LRG Import (all species)

Importing the latest version of Locus Reference Genomic dataset

Gene and Transcript Adaptor support for fetch_all_by_Source() (all species)

GeneAdaptor and TranscriptAdaptor will support the retrieval of their respective feature objects by the new source column

SQLite Support (all species)

The Ensembl core API will support SQLite databases. This work has been contributed by the Anacode team at the WTSI.

patch_74_75a.sql - schema_version update in production db (all species)

Update schema_version in meta table to 75.

patch_74_75_c.sql (all species)

Adding a new table genome_statistics

Populated during the production run, it contains basic statistics on the number of genes, the length of the genome or the number of prediction

patch_74_75_e.sql (all species)

Attrib related tables do not allow duplicates

Unique key constraints added to enforce this

External database references update (multiple species)

Xrefs update for:

human, sloth, seq squirt, chicken, kangaroo rat, stickelback, coelacanth, wallaby, pika, medaka, hyrax, megabat, fugu, tarsier, alpaca, dolphin, tree shrew, zebrafish

patch_74_75_a.sql - schema_version update in ontology db (all species)

Update schema_version in meta table to 75.

patch_74_75b.sql - longer code in attrib_type (all species)

'code' column in master_attrib_type table expanded

patch_74_75_f.sql - longer code (all species)

'code' column in attrib_type table longer

Stable ID lookup (all species)

Stable ID lookup provided for REST services

patch_74_75_a.sql - schema_version update (all species)

Update schema_version in meta table to 75.

patch_74_75_b.sql - transcript source (all species)

Adding the source column to the transcript table

patch_74_75_d.sql - default source for transcripts (all species)

The new Transcript source column required a default value, that is now set to ensembl.

Release 74

LRG Import (all species)

Importing the latest version of Locus Reference Genomic dataset

Global UniParc xref update (all species)

UniParc, as xref source, is randomly scattered in the configuration file. It is specified as source for some species but not for all.

UniParc will be used for all species with no exception.

External database references update (multiple species)

Xrefs update for:

human, mousesarcophilus_harrisii, otolemur_garnettii, equus_caballus, pongo_abelii, ornithorhynchus_anatinus, monodelphis_domestica, mustela_putorius_furo, xiphophorus_maculatus, macaca_mulatta, tetraodon_nigroviridis, bos_taurus, anolis_carolinensis, pan_troglodytes, gadus_morhua, loxodonta_africana, cavea_porcellus, callithrix_jacchus, sus_scrofa, rattus_norvegicus, meleagris_gallopavo, ailuropoda_melanoleuca, xenopus_tropicalis, nomascus_leucogenys, myotis_lucifugus, oreochromis_niloticus

Replacement of BiotypeMapper by SO mapper and EnsEMBL ORM API (all species)

The module Bio::EnsEMBL::Utils::BiotypeMapper encodes both the logic to convert biotypes to sequence ontology terms and the logic to deal with biotype groups.

As for the mapping between biotypes and SO terms, we will replace BiotypeMapper with a more dedicated SequenceOntologyMapper whose role is to convert EnsEMBL feature or related objects to SO terms.

The responsibility to deal with biotype groups in the production database will be granted to the Biotype and the corresponding Manager object in the EnsEMBL ORM framework.

Archive stable IDs (all species)

Archive stable IDs in the stable id lookup DB.

Stable ID lookup (all species)

Stable ID lookup provided for REST services

New GenomeContainer (all species)

New GenomeContainer module to replace the AssemblyAdaptor

More generic container for genome related information

Including:

- various annotation statistics

- various assembly lengths and slices

patch_73_74a.sql - schema_version update in production db (all species)

Update schema_version in meta table to 74.

patch_73_74_a.sql - schema_version update in ontology db (all species)

Update schema_version in meta table to 74.

Ensembl VM Build (all species)

The Ensembl Virtual Machine applicance will be updated to version 74.

patch_73_74_a.sql - schema_version update (all species)

Update schema_version in meta table to 74.

patch_73_74_b.sql - dnac removal (all species)

Remove dnac table which is not used any more.

patch_73_74_c.sql - unconventional_transcript_association removal (all species)

Remove unconventional_transcript_association table which is not used any more.

patch_73_74_d.sql - QTL removal (all species)

Remove of the qtl tables (qtl, qtl_feature, qtl_synonym) which are not used any more.

patch_73_74_e.sql - Canonical_annotation removal (all species)

Removal of the canonical_annotation column in the gene table, as it is not used any more.

patch_73_74_f.sql - Pair_dna_align_feature removal (all species)

Removal of the pair_dna_align_feature_id column in the dna_align_feature table, as it is not used any more.

patch_73_74_g.sql - Adding transcript index to transcript_intron_supporting_evidence (all species)

Adding an index on transcript id to transcript_intron_supporting_evidence to
speed up retrieval of supporting features from a Transcript object

Retirement of dnac related material (all species)

Match the removal of table dnac, by retiring misc-scripts/utilities/dna_compress.pl (driver script to populate and test the experimental dnac table of ensembl) and, correspondigly, the module Bio::EnsEMBL::DBSQL::CompressedSequenceAdaptor.

Retirement of unconventional transcript association adaptor (all species)

Bio::EnsEMBL::DBSQL::UnconventionalTranscriptAssociationAdaptor will be retired, to match patch_73_74_c.sql which removes the table unconventional_transcript_association.

patch_73_74_h.sql - Adding unique index to alt_allele(gene_id) (all species)

Adding an index on gene_id in alt_alelle to enforce a 1 gene 1 group policy.

Release 73

LRG Import (all species)

Importing the latest version of Locus Reference Genomic dataset

Stable ID cleanup (all species)

Removal of confusing stable id history to provide a more useful lookup

Stable ID lookup (all species)

Stable ID lookup provided for REST services

Misc-scripts cleanup (all species)

Removing a number of files and directories from ensembl checkout misc-scripts

Some have been moved to ensembl-production, others are simply deprecated and not maintained any more

patch 72_73_a.sql - schema version update for ontology (all species)

Update schema_version in ontology meta table to 73.

External database references update (multiple species)

Xref updates for

  • homo sapiens
  • danio rerio
  • pan troglodytes
  • otolemur garnettii
  • gadus morhua
  • dasypus novemcinctus
  • taeniopygia guttata
  • ictidomys tridecemlineatus
  • pelodiscus sinensis
  • canis familiaris
  • sus scrofa

Ensembl VM Build (all species)

The Ensembl Virtual Machine applicance will be updated to version 73.

patch 72_73_a.sql - schema version update (all species)

Update schema_version in meta table to 73.

Object_xref enum expansion (all species)

Object_xref ensembl_object_type expanded to include marker

patch 72_73a.sql - schema version update for production (all species)

Update schema_version in production database meta table to 73.

Release 72

ensembldb.ensembl.org will be hosted on 3306 by default (all species)

We will make ensembldb.ensembl.org available on ports 3306 and 5306. For access to databases prior to release 48 this server will be made available on port 4306.

LRG Import (Human)

Importing the latest version of Locus Reference Genomic dataset

Production script movement (all species)

A number of scripts are beginning a migration from our core checkout into a new ensembl-production checkout. These scripts are viewed as required only for internal production work. Scripts will be removed from misc-scripts in release 73.

ping_ensembl.pl supports alternative database installations (all species)

ping_ensembl.pl can query multiple resources other than the default ensembldb.ensembl.org instance.

patch 71_72_a.sql - schema version update (all species)

Update schema_version in meta table to 72.

patch 71_72_b.sql - associated_xref (all species)

Schema support for associated xrefs

Ensembl VM Build (all species)

The Ensembl Virtual Machine applicance will be updated to version 72.

External database references update (multiple species)

External database references will be updated for:

  • Human
  • Mouse
  • Pig
  • Ciona savigny
  • Hedgehog
  • Mouse lemur
  • Gorilla
  • Shrew
  • Lamprey
  • Tenrec

Release 71

LRG Import (Human)

Importing the latest version of Locus Reference Genomic dataset

patch 70_71_b.sql - add mapping set primary key (all species)

Schema file and patches back in sync

The mapping_set table should have a primary key

Ensembl VM Build (all species)

The Ensembl Virtual Machine applicance will be updated to version 71.

patch 70_71_a.sql - schema version update (all species)

Update schema_version in meta table to 71.

External database references update (multiple species)

External database references will be updated for:

  • Human
  • Zebrafish
  • Ciona intestinalis
  • Anole lizard
  • Dolphin
  • Guinea pig
  • Wallaby
  • Coelacanth
  • Tarsier
  • Rock hyrax
  • Pika
  • Fugu
  • Sloth
  • Megabat
  • Alpaca
  • Kangaroo rat
  • Stickleback
  • Medaka
  • Shrew

Release 70

EMBL and Genbank Dumps (all species)

EMBL and Genbank dumps for all species.

patch 69_70_b.sql - add mapping set history (all species)

Update mapping_set to store history over several releases

patch 69_70_c.sql - Datatype Consistency (all species)

A number of data types in other tables have diverged from the field's original specification preventing foreign key links from being created. Data types have been normalised where inconsistency was found. Affects data_file, object_xref and dependent_xref.

Enhanced feature counting (all species)

BaseFeatureAdaptor (and by extension, all feature adaptors), has acquired the get_by_Slice_constraint method. Under certain situations the generic_count method is too slow. If this should occur, get_by_Slice_constraint can be used for rapid feature counting within the given Slice object. This includes features which are partially overlapping with the boundaries of the Slice.

LRG Import (all species)

Importing the latest version of Locus Reference Genomic dataset and updates to process LRG's 1.7 XML schema.

Pilot and strict 1000Genomes Accessible Genome Data Import (Human)

1000Genomes' accessible genome data, ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase1/analysis_results/supporting/accessible_genome_masks/, has been imported as a set of SimpleFeature in the otherfeatures human database. The pilot and strict datasets have been used.

Assembly Mapping Dog; BROAD2 to CanFam3.1 (Dog)

Production of an assembly mapping to convert coordinates from dog's BROAD2 assembly to CanFam3.1.

Assembly Mapping Pig; Sscrofa9 to Sscrofa10.2 (Pig)

Production of an assembly mapping going from pig's old Sscrofa9 assembly to Sscrofa10.2

Assembly Mapping Rat; RGSC3.4 to Rnor_5.0 (Rat)

Providing an assembly mapping for rat's old assembly RGSC3.4 to Rnor_5.0

patch 69_70_a.sql - schema version update (all species)

Update schema_version in meta table to 70.

Transcript naming update (multiple species)

The name of a transcript is now inferred from the gene name.

Transcript names will be updated for:

  • C. intestinalis
  • Cow
  • Panda
  • Tetraodon
  • Xenopus
  • Macaque
  • Rabbit

External database references update (multiple species)

External database references will be updated for:

  • Human
  • Mouse
  • Pig
  • Zebrafish
  • Chicken
  • Marmoset
  • Turkey
  • Zebra finch
  • Elephant
  • Tilapia
  • Microbat
  • Rat

Ensembl VM Build (all species)

The Ensembl Virtual Machine applicance will be updated to version 70.

Release 69

EMBL and Genbank Dumps (all species)

EMBL and Genbank dumps for all species.

external database references update (multiple species)

xrefs will be updated for:

  • Ferret
  • Platyfish
  • Human
  • Zebrafish
  • Pig
  • Opossum
  • Platypus
  • Orangutan
  • Horse
  • Gibbon
  • C. intestinalis
  • Cow
  • Panda
  • Tetraodon
  • Xenopus
  • Macaque
  • Rabbit

Karyotype_rank (multiple species)

A karyotype_rank attribute has been added for species with chromosomes. This allows us to store an ordered list of the seq regions (i.e. chromosomes) that should be drawn in an Ensembl karyotype.

Previously this variable (ENSEMBL_CHROMOSOMES) was stored in the species' .ini file, and Ensembl-based sites can continue to use this configuration as an alternative. However if you do switch to using the karyotype_rank attrib in your databases, you will need to comment out the version in the ini file, as it will get added to the chromosome array rather than merged into it.

Delete unused density features (all species)

New density features have been introduced and unused ones are being retired

logic names 'knowngenedensity' and 'genedensity' are being replaced by 'codingdensity', 'pseudogenedensity' and 'noncodingdensity'

patch 68_69_a.sql - schema version update (all species)

Update schema_version in meta table to 69.

Release 68

EMBL and Genbank Dumps; restructuring (all species)

EMBL and Genbank dumps for all species. This release sees a change in the structure of these files. We now create 1 file per chromosome and then a file which holds all other non-chromosomal regions. This mimicks the current FASTA structure.

New Ensembl virtual machine (all species)

We now have a new virtual machine with all the Ensembl APIs and the VEP (Variant Effect Predictor) pre-installed. More information can be found in the Ensembl Tools section.

Meta key addition and retirement (all species)

The following meta keys are retired

  • species.short_name
  • species.ensembl_common_name
  • species.ensembl_alias_name

The following meta keys will added

  • species.url
  • species.display_name

 

Updated GO Projection rules (all species)

GO projection rules have been updated after consultation with GOA. The following rules will be applied

  • No projection between mammals and fish
  • Allowing EXP as a valid evidence code

In conjunction with these rules we will not terms which are children of the following when projecting from mammals to birds & platypus deriving from these terms

  • GO:0032501 multicellular organismal process
  • GO:0007610 behaviour
  • GO:0048856 anatomical structure development
  • GO:0051704 multi-organism process

 

Soft-masked FASTA files (all species)

Genomic regions are now dumped with repeats soft-masked in addition to our hard-masked and unmasked files. These are available on our FTP site. The type is dna_sm.

External database references update (all species)

Xref update to Human, Mouse and Zebrafish

 

 

New Ensembl virtual machine (all species)

Updated version of our VM applicance with Ensembl APIs and the VEP (Variant Effect Predictor) pre-installed. More information can be found in the Ensembl Tools section.

Updated Xref storage API and schema (all species)

The xref API and schema has been modified to prevent unintentional insertion of duplicate records into the xref schema.

patch 67_68_a.sql - schema version update (all species)

Update schema_version in meta table to 68.

patch 67_68_b.sql - xref unique constraints (all species)

Enforcement of existing unique constraints in the xref schema storage (xref and object_xref) by removing fields which were allowed to be NULL.

Improved external name API (all species)

Improved external name methods from Gene to avoid excessive compute times when searching with RefSeq identifiers.

Efficiency boost for xref lookups (all species)

Gene, Transcript and Translation all provide fetch_all_by_external_name methods. These methods allow user-supplied wildcards, but many external names contain characters that are SQL wildcards too.

For reasons of speed, we have automatically escaped an underscore in position three of any external name. For users who know what they are asking for, this escaping can be turned off with an override flag supplied as the last argument to the fetch_all call.

patch_67_68_d.sql - Flagging Splice Canonical Introns (all species)

Brings in a new field into the intron_supporting_evidence table which allows the API to flag an intron as having canonical splicing.

patch_67_68_e.sql (all species)

Patch identifier patch_67_68_b.sql originally did not apply a unique index to version. This has been altered but this patch is made available for users who patched with previous version of b to alter the unique index. B has also been modified accordingly.

patch 67_68_c.sql - updated intron storage schema (all species)

Intron supporting feature schema is to be updated to hold intron locations

Release 67

patch_66_67_b.sql - drop stable ID views (all species)

The stable ID views, introduced for release 65 as a way of providing a degree of backward compatibility, are dropped with this release.

New Ensembl virtual machine (all species)

We now have a new virtual machine with all the Ensembl APIs and the VEP (Variant Effect Predictor) pre-installed. More information can be found in the Ensembl Tools section.

patch 66_67_a.sql - schema version update (all species)

Update schema_version in meta table to 67.

external database references update (all species)

Xref update for human, mouse, zebrafish, cape rock hyrax, large flying fox, zebra finch, gray short-tailed opossum, dog, African savanna elephant, giant panda, green anole lizard, turkey

 

 

patch_66_67_c.sql - intron_supporting_evidence (all species)

Formalisation of the exon relationship to create an intron. This allows us to score the intron and therefore give a confidence rating.

patch_66_67_d.sql - New evidence types (all species)

Adding ANNOTATED as an evidence type

patch_66_67_e.sql - Indexing canonical_transcript_id (all species)

Missing index. Added for performance reasons

GeneAdaptor methods fetch_all_by_display_label and fetch_by_display_label (all species)

New GeneAdaptor method fetch_all_by_display_label to retrieve all genes which have the given display label.

Change to fetch_by_display_label - Returns the gene which has the given display label or undef if there is none. If there are more than 1, the gene on the reference slice is reported or if none are on the reference, the first one is reported.

Release 66

Support for trinomial names (all species)

The API will be updated to allow for trinomial named species. This will affect Bio::EnsEMBL::Registry as well as Bio::EnsEMBL::MetaContainer.

Deprecation of Bio::EnsEMBL::MetaContainer::get_Species() (all species)

Bio::EnsEMBL::MetaContainer::get_Species() has been deprecated due to trinomial support. Any calls for scientific names should be made via the meta items already made available from Bio::EnsEMBL::MetaContainer.

FASTA Dumping (all species)

New efficient FASTA dumping module

Xref projections (all species)

Gene ontology (GO) identifiers and gene names will be projected for all species.

Splicing events (all species)

The ASTD project computationally predicted genes in a similar way to Ensembl every release with a focus on alternative mRNA structures (splicing events, poly(A) sites, TSS) and features (ppt, exon-exon junction types)

Since 2010, the storage and display of the alternative information is now an entire part of Ensembl for the following species:
    - Homo sapiens,
    - Mus musculus,
    - Rattus norvegicus,
    - Danio rerio,
    - Caenorhabditis elegans,
    - Drosophila melanogaster

These data have been updated for this release for the species listed above.

external database references update (all species)

Xref update for human, mouse, western clawed frog, American pika, cat, guinea pig, dasypus_novemcinctus, Philippine tarsier, alpaca, two-fingered sloth, kangaroo rat, bottlenosed dolphin

patch_65_66_a schema version update (all species)

Update schema_version in meta table to 66.

new schema patching script (all species)

The script used for patching schemas, ensembl/misc-scripts/schema_patch.pl, will be replaced by a new script, ensembl/misc-scripts/schema_patcher.pl, which is slightly smarter. Note that this is a reimplementation from scratch and that the new script has different command line options compared to the old script.

patch_65_66_f.sql Defaults synchronisation between tables.sql and patches (all species)

A number of columns did not have their default values removed at the same time as the main schema was updated.

patch_65_66_b.sql external_db_id definition change (all species)

 

We're using too high values in external_db.external_db_id for the current SMALLINT, and with the web interface we're using internally to add new entries, we also need this field to be AUTO_INCREMENT.

 

assembly mapping between Btau_4.0 and UMD3.1 (Cow)

Assembly mapping for cow between Btau_4.0 and UMD3.1 assemblies

patch_65_66_c.sql Reorder an index in unmapped_object. (all species)

 

The unique_unmapped_obj_idx index in the unmapped_object table is ineffective when querying the table.  Its first part, for example, partly overlaps with the id_idx index.  A reordering was suggested by the Ensembl Regulation team.

 

Support for single databases from load_registry_from_url (all species)

Bio::EnsEMBL::Registry->load_registry_from_url() has been extended to support single database specifications as a way of avoiding having to write a registry file to load 1 database.

method fetch_all added to TranslationAdaptor (all species)

method fetch_all added to TranslationAdaptor

patch_65_66_d.sql add index to ontology_xref (all species)

Add index on object_xref_id column in ontology_xref

patch_65_66_e.sql disallow nulls from external_db_id (all species)

Nulls are no longer allowed in the column xref.external_db_id

%_stable_id views to be removed in release 67 (all species)

The views (%_stable_id) in the Ensembl Core schema will be removed in release 67.

Release 65

Merge of stable_id tables with their object tables (all species)

patch_64_65_b.sql

Schema patch to merge stable_id tables with exon, gene, operon, operon_transcript, translation and transcript tables

Changes to the core API, stable_id mapping scripts, xref_mapping, test modules.

Xref projections (all species)

Gene ontology (GO) identifiers and gene names will be projected for all species. Modify Modify projection code to replace UniProt IDs with display labels where applicable.

LRG Import (Human)

Import of new LRG sequences

Memory leak fixes (all species)

A number of leaks have been found & fixed in the Ensembl API caused by circular references and unintentional object usage.

Schema change; new enum for xref.info_type (all species)

The enum field `xref`.`info_type` has been given a new value called CHECKSUM to support xrefs assigned on the basis of a checksum mapping.

Region Report tool (all species)

A new tool plus supporting libraries for creating summaries of requested chromosomal regions.

external database references (all species)

Human, Mouse, Pig, Ciona Intestinalis, Cow, Pig, Platypus, Chick, Dog, Horse, Tetraodon external database references have been updated. 

 

Splicing events (multiple species)

The ASTD project computationally predicted genes in a similar way to Ensembl every release with a focus on alternative mRNA structures (splicing events, poly(A) sites, TSS) and features (ppt, exon-exon junction types)

Since 2010, the storage and display of the alternative information is now an entire part of Ensembl for the following species:
    - Homo sapiens,
    - Mus musculus,
    - Rattus norvegicus,
    - Danio rerio,
    - Caenorhabditis elegans,
    - Drosophila melanogaster

These data have been updated for this release for the species listed above.

Retrieval of a Transcript's Gene (all species)

Support has been added to retrieve the Bio::EnsEMBL::Gene from an instance of Bio::EnsEMBL::Transcript.

Support for Slice Retrieval by a Location String (all species)

Bio::EnsEMBL::DBSQL::SliceAdaptor can retrieve a Slice for a toplevel location string

Release 64

Xref projections (all species)

Gene ontology (GO) identifiers and gene names have been projected for all species including the new lamprey and Tasmanian devil species.

Xrefs updated (all species)

Cross-references (xrefs) to external databases were updated for human, mouse, sea squirts Ciona intestinalis and Ciona savignyi, Madagascan hedgehog tenrec, Western European hedgehog, mouse lemur, platypus, bushbaby, shrew, and squirrel.

schema change (all species)

is_ref will be added to the alt_allele table to show which is the reference gene.

Schema version update (all species)

patch_63_64_a.sql

update schema version to 64

LRG import (Human)

Import of new LRG sequences 

Linkage_type change in ontology_xref (all species)

Change to linkage_type column in table ontology_ref. Values to be tested in healthchecks.

patch_63_64_d.sql

Release 63

xref projection (all species)

Project GO ids and gene names to species. Make alterations to zebrafish projections.

EMBL & Genbank dumps (all species)

EMBL & Genbank dumps for all species

Update schema version (all species)

 

# Description:

#   Update schema_version in meta table to 63.

 

UPDATE meta SET meta_value='63' WHERE meta_key='schema_version';

 

# Patch identifier

INSERT INTO meta (species_id, meta_key, meta_value)

  VALUES (NULL, 'patch', 'patch_62_63_a.sql|schema_version');

 

Indexing changes for core database. (all species)

 

Change stable Id version to not null, default 1 in exon_stable_id, gene_stable_id, transcript_stable_id, translation_stable_id, gene_archive.

Create unique index on stable_id and verision for gene_archive.

Create a unique index for table umapped_object. 

 

Remove field dbprimary_acc_linkable from external_db table. (all species)

Remove field dbprimary_acc_linkable from external_db table.

Removal of lowercase letter at the end of all database names (all species)

For release 63 it has been decided to remove the lowercase letter at the end of all database names as it is confusing for users and provides little meaning about actual data changes.

Update xrefs for core databases (all species)

Update xrefs for Human, Mouse, Rat, Pig, Macaque, Chimp, Orangutan, Fugu and Stickleback.

API web documentation overhaul (all species)

Replace PDoc system with Doxygen + Perl Filter to produce API reference web pages.

xref sources to be moved to gene level (all species)

The following External database sources have been moved up to the Gene level :-

DBASS3, DBASS5, EntrezGene, miRBase, RFAM, UniGene, Uniprot_genename, WikiGene, MIM_GENE and  MIM_MORBID.

Release 62

Bio::EnsEMBL::DBFile::FileAdaptor (all species)

A new base class for accessing data from flat files

Bio::EnsEMBL::DBFile::CollectionAdaptor (all species)

A new class to access Collection Feature data stored in flat files.

patch_61_62_a: Schema version patch (all species)

Patch file patch_61_62_a.sql, updates the schema version of a core database to 62.

Ontology database (all species)

Database ensembl_ontology_62 with latest available GO, SO, and EFO ontologies. Synonyms will now be included in a new 'synonym' table.

Schema diagrams for online documentation (all species)

Schema diagrams for online for core database documentation.

patch_61_62_b: synonym field extension (all species)

Patch file patch_61_62_b.sql, extends field synonym in external_synonym table to 100 chars.

patch_61_62_c: index for db_name, db_release (all species)

Patch file patch_61_62_c.sql adds unique index to db_name, db_release fields in external_db table.

Xrefs (Zebrafish)

Update external database references.

xref projection (all species)

Project GO ids and gene names to species. Make alterations to zebrafish projections.

EMBL/Genbank dumps (all species)

EMBL & Genbank dumps for all species

patch_61_62_d: remove field display_label_linkable (all species)

Patch file patch_61_62_d.sql removes field display_label_linkable from table external_db.

Import of LRG sequences (Human)

Newly published LRG sequences will be imported

Ontology API (all species)

Addition of fetch_all_by_name() method to the OntologyTermAdaptor to fetch ontology terms by their names or synonyms. Additional synonym() method for OntologyTerm objects to get their synonyms.

xrefs (Human)

Update human external database references.

xrefs (Mouse)

Update external database references

Release 61

seq region synonyms (all species)

New table seq_region_synonym added to allow multiple names for sequence regions.

external database references (all species)

Human, mouse, rat and tree shrew will be updated.

GO term and gene name projections (all species)

Gene display names and GO terms will be projected from high-coverage species to those with lower coverage.

Ontology database (all species)

The Ensembl Ontology database will as usual be populated with the latest available versions of the

  • Gene Ontology (GO)
  • Sequence Ontology (SO)
  • Experimental Factor Ontology (EFO)

embl and genbank dumps (all species)

Onlt the reference sequence will be dumped in the main directory for embl and genbank. Unique non-reference regions(haplotype/par regions) will now be dumped in a subdirectory and only contain the unique regions.

Release 60

Ontology database (all species)

A new ontology database ("ensembl_ontology_60") will be built using the latest data from GO and SO.

Gene name and GO term projections (all species)

Gene names and GO xrefs will be projected from species where there is high coverage to species where there is lower coverage. Panda will be included as a target for these projections.

external database references (all species)

Update external database references for human, mouse and Xenopus

GO Xrefs are now Ontology Xrefs (all species)

The go_xref table is renamed to ontology_xref. The Bio::EnsEMBL::GoXref Perl module is renamed to Bio::EnsEMBL::OntologyXref.

Release 59

external database references (all species)

Update External database references for:-

  • Human
  • Mouse
  • Cow
  • Chicken

New species name meta-values with corresponding helper methods (all species)

A set of new meta key-value pairs are inserted into all Core databases:

  • species.production_name (a string that may be used to refer to a particular species in e.g. database tables or file names)
  • species.scientific_name (the full bi- or trinomial scientific name of the species)
  • species.short_name (a short string, often based on the common name, useful for labels in GUIs etc.)

For each of these, the Bio::EnsEMBL::DBSQL::MetaContainer class now also contains a get_* method for retrieval of the corresponding meta value (get_short_name(), etc.). There is also a new get_common_name() method.

Mouse IKMC xrefs and features (all species)

Support mouse IKMC (International Mouse Knockout Consortium) links by creating a set of simple features to show the genomic extent of the knockouts.

Update Amazon data sets (all species)

Update Amazon data sets for MySQL and FASTA dumps.

Gene name and GO term projections (all species)

Assign gene names and GO terms to species where they are not well covered by projection from well-annotated species, using Compara homologies.

Schema change (all species)

We will have the following schema patches to the Ensembl Core schema:

  1. Update schema version, as usual.
  2. Add new exception types ('PATCH_NOVEL' and 'PATCH_FIX') to the assembly_exception table. This is to allow for patched assemblies.
  3. Modify the splicing_event table so that instead of a 'type' field there is an 'attrib_type_id' pointing to the attrib_type table. The short enumerated codes were too terse.
  4. A unique index in the object_xref table ('object_type_idx') is being extended to include the 'analysis_id'. This is to allow two object Xrefs for the same object using two different analyses.
  5. A new meta key 'schema_type' (with value 'core' for Ensembl Core databases) will be inserted into all Core databases.

Drosophila melanogaster update (all species)

Update of D. melanogaster gene set to release 5.25 (FlyBase 2010_02).

Ontology database (all species)

We will provide the ensembl_ontology_59 database with updated data from Gene Ontology (GO) and Sequence Ontology (SO).

Meta table changes (all species)

These changes are intended to solidify the requirements for names in Ensembl and will reduce the amount of name conversion which occurs in the codebase.

meta key usage required stable regular expression example value
species.production_name Used for a computing scenario e.g. writing a file to disk. yes yes $[a-z0-9_]+^ homo_sapiens
species.scientific_name The full name of the species, which should replace the call MetaContainer->get_Species()->binomial() yes no - Homo sapiens
species.common_name The common name of the species, which can equal the value from taxonomy no no - human
species.short_name A name which is short enough to be used in space-constrained areas (such as tabs on the web site) yes no - human

Future Plans

Read about our future plans on our blog!