News for Mouse Ensembl Release 81 (July 2015)

News categories

New web displays and tools

Trackhub settings support

In this release we have added support for trackhub visibility settings; in other words, tracks that are turned on by default in the hub's trackDb.txt file should automatically be shown in Ensembl.

The only exception is for hubs that we configure internally, such as the Genome Reference Consortium GRIT hub. For these, all tracks will be hidden by default, but you can find them by searching in the Control Panel.

Transcript sequence markup

Transcript sequences can now be marked up to show exons as alternating upper and lower case characters, rather than grey/blue text. Simply check the "Show exons as alternating upper/lower case" box in the "Configure this page" panel on Transcript cDNA or Transcript Protein pages.

This markup option will also carry over to the sequence export if RTF format is chosen.

New species, assemblies and genebuilds

Mouse: assembly updated to GRCm38.p4

The mouse genome assembly was updated to GRCm38.p4 and the assembly information in all mouse databases has been altered accordingly. This minor assembly update contains 30 assembly patches. The DNA sequence for the primary assembly (chromosomes, unlocalized scaffolds and unplaced scaffolds) remains unchanged.

Vega Mouse annotation updated

Manual annotation of mouse from Havana has been updated and contains the data released in Vega 61

New regulation data

Mouse regulatory Build update

The Regulatory Build on Mouse was re-computed, converting the "old style" build to the "new style" build, as was done on human in E!76. All Regulatory Builds in Ensembl are now updated to the new style.

We took the opportunity to increase the number of cell types to 8.

API and schema changes

Schema update: Storing sample data

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

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.

Other updates

Compara

Schema version update

80 -> 81

Pairwise alignments: human and mouse patches

  • Human is patched to GRCh38.p3, so

    • we will upload human_ref-to-human_patches alignments done by Genebuilders 
    • we will run human_patches-to-high_coverage_species lastz alignments

  • Mouse is patched to GRCm38.p4, so

    • we will upload mouse_ref-to-mouse_patches alignments done by Genebuilders 
    • we will run mouse_patches-to-high_coverage_species lastz alignments

ProteinTrees and homologies

GeneTrees (protein-coding) with new/updated genebuilds and assemblies

 -- all-vs-all blastp (ncbi-blast-2.2.30+)
 -- Clustering using hcluster_sg
 -- Multiple sequence alignments using MCoffee (Version_9.03.r1318) or Mafft (mafft-7.221)
 -- Phylogenetic reconstruction using TreeBeST
 -- Homology inference
 -- Pairwise gene-based dN/dS scores for high coverage species pairs only (both on orthologues and paralogues) (codeml/PAML v4.3)
 -- GeneTree stable ID mapping
 -- Per family gene dynamics using CAFE (v2.2)

Protein Families

Updated MCL families including all Ensembl transcript isoforms (including human non-reference haplotypes) and newest Uniprot Metazoa.

 -- Getting distances by NCBI BlastP (v.2.2.30+)
 -- Clustering by MCL (v.14-137)
 -- Multiple Sequence Alignments with MAFFT (v.7.221)
 -- Family stable ID mapping

ncRNAtrees and homologies

Classification based on Rfam models (v11.0)
Multiple sequence alignments with Infernal
Phylogenetic reconstruction using RAxML
Phylogenetic reconstruction using FastTree2 and RAxML-Light for very big families
Additional multiple sequence alignments with Prank (w/ genomic flanks)
Additional phylogenetic reconstruction using PhyML and NJ
Phylogenetic tree merging using TreeBeST
Per family gene dynamics using CAFE
Homology inference
Secondary structure plots

Compara dumps

  • EMF / Fasta / OrthoXML / PhyloXML dumps for ProteinTrees + PhyloXML dumps for CAFE ProteinTrees
  • EMF / Fasta / OrthoXML / PhyloXML dumps for ncRNAtrees + PhyloXML dumps for CAFE ncRNAtrees

Core

External database references update

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)

Ensembl VM Build

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

LRG Import

Importing the latest version of Locus Reference Genomic dataset

patch_80_81_a.sql - schema_version update

Update schema_version in meta table to 81.

patch_80_81_a.sql - schema_version update in ontology db

Update schema_version in meta table to 81.

patch_80_81a.sql - schema_version update in production db

Update schema_version in production database to 81.

Stable ID lookup

Stable ID lookup provided for REST services

Includes lookup for RefSeq and CCDS entries

UTR features in the REST API

UTR features can be retrieved using the REST API

Band information in the REST API

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

New UTR, CDS and ExonTranscript features

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

GFF3 dumps

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

Regulation

patch_80_81_c Drop experiment.date

The experiment.date field has been dropped from the funcgen schema and the related Bio::EnsEMBL::Funcgen::Experiment::date method has been deprecated.

Collection Files replaced by BigWigs

The Funcgen density maps, which were previously stored in an in-house flat file format (Collection Files) were ported to the more common standard, BigWig.

The Funcgen API now provides only a path to the files, which can be read using the Ensembl::IO repository. 

patch_80_81_a.sql - schema_version update

patch_80_81_a.sql - schema_version update

patch_80_81_b.sql|add gender 'mixed' to table cell_type

patch_80_81_b.sql|add gender 'mixed' to table cell_type 

Genebuild

Mouse: GRCm38.p4 Karyotype Bands

Karyotype bands were updated in regions overlapping patches

Update to Ensembl-Havana mouse GENCODE gene set

Updated Ensembl-Havana mouse gene set. This gene set is a merge of complete Ensembl gene models and the latest Havana gene annotation. All CCDS genes are included in this gene set.

The mouse GRCm38.p4 gene annotation is also included:

The patches for GRCm38.p4 were annotated using a combination of annotation projected from the primary assembly and annotation derived from cDNA and protein alignment evidence. Annotation of the patches is stored in the core database.

Mouse: updated cDNA alignments

A new cdna database was created for e80: The latest set of cDNAs for mouse (as of Month 2015) from the European Nucleotide Archive and NCBI RefSeq (release nn) were aligned to the current genome using Exonerate.

Updated mouse otherfeatures db: New CCDS import

This release of the mouse gene set also includes 23,830 transcript models as part of an updated version (May 2015) of CCDS

Mouse: updated RefSeq gene import

The imported RefSeq gene set was updated in the mouse otherfeatures database. Please note that RefSeq annotates gene models on cDNA sequence and not on the reference genome, meaning that when users choose to translate the RefSeq transcripts off the reference genome that the translations may contain stop codons.

Mouse clone import

Mouse clone libraries have been imported from the NCBI clone database. to replace previous DAS tracks. The tracks for the clones can be found under "Clones and misc regions" in the configuration menu, while the coordinates for the BAC ends can be found as tracks under "Simple features", also in the configuration menu.

Upgrade remaining species to rnaseq matrix

For some species we have RNASeq data but have not yet displayed options in an RNASeq matrix for the users. This requires changes to the analysis_description, analysis_web_data and web_data tables in the ensembl_production database

Production

EMBL and Genbank Dumps

EMBL and Genbank dumps for all species.

Ensembl 81 mart databases

  • Ensembl Genes 81
    • Human assembly updated from GRCh38.p2 to GRCh38.p3
    • Mouse assembly updated from GRCm38.p3 to GRCm38.p4
  • Ensembl Variation 81
    • Human assembly updated from GRCh38.p2 to GRCh38.p3
    • Mouse assembly updated from GRCm38.p3 to GRCm38.p4
    • Added new structural variation species Sheep (Ovis aries)
  • Ensembl Regulation 81
    • New mouse regulation build data
  • Vega 61
    • Human assembly updated from GRCh38.p2 to GRCh38.p3
    • Mouse assembly updated from GRCm38.p3 to GRCm38.p4

External reference projection

Gene ontology (GO) identifiers and gene name projection to all species.

FASTA & GTF dumps

FASTA & GTF dumps for all the species

Variation

Phenotype data updates

  • Human phenotype data has been updated from different sources including NHGRI-EBI GWAS, OMIM, ClinVar, UniProt and Decipher.
  • OMIA data for Cow, Dog, Horse, Sheep
  • RGD data for Rat
  • AnimalQTL for Cow, Horse, Chicken, Pig, Sheep
  • IMPC data (release 3.1) for Mouse

Structural variations

  • Added new studies and updated other studies from DGVa

Web

replace i icon with ? icon

The "i" icon when clicked gives you the help/documentation page has been replaced with a new "?" icon.

The "i" icon in the tracks configuration has been left unchanged as this is more information rather than help.

Public plugins sqlite and sge_blast removed

The said two plugins, one for SQLite support for user db and other for SGE BLAST, were outdated and have been removed from the public-plugins repository.

Retirement of archives 67 and 59

This release cycle we will be retiring archive 67 (May 2012) in accordance with our three-year rolling retirement policy. Due to the arrival of GRCz10 in Ensembl 80 we will also be retiring archive 59 (Aug 2010) which currently shows Zebrafish Zv8 annotation.The data will remain available on our public database server; only the web interfaces will be removed.

User accounts/session database configuration changed

Database used for user accounts and sesison records was configured using the conf/SiteDefs.pm configurations as below:

$SiteDefs::ENSEMBL_USERDB_TYPE = 'mysql';
$SiteDefs::ENSEMBL_USERDB_NAME = 'ensembl_accounts';
$SiteDefs::ENSEMBL_USERDB_USER = 'mysqluser';
$SiteDefs::ENSEMBL_USERDB_HOST = 'localhost';
$SiteDefs::ENSEMBL_USERDB_PORT = 3306;
$SiteDefs::ENSEMBL_USERDB_PASS = '';

These configurations have been removed and now the database is configured by adding configurations in conf/ini-file/MULTI.ini as below:

[databases]
DATABASE_ACCOUNTS = ensembl_accounts
DATABASE_SESSION = ensembl_accounts

[DATABASE_ACCOUNTS]
HOST = localhost
PORT = 3306
USER = mysqluser
PASS =

[DATABASE_SESSION]
HOST = localhost
PORT = 3306
USER = mysqluser
PASS =

Changes to the code can be seen here: