WormBase Release WS263

We would like to announce the availability of the WormBase WS263 release on the WormBase website and FTP.

Some of the highlights of this release are:

New Pristionchus Assembly and Gene Set

The new data made available through WormBase is described in “Single-Molecule Sequencing Reveals the Chromosome-Scale Genomic Architecture of the Nematode Model Organism Pristionchus pacificus by Christian Roedelsperger, et al. in Cell.

ID mapping was carried out to try and preserve the existing IDs. The published IDs were also incorporated into the database so that they are searchable on wormbase.org.

New PantherDB data

the PantherDB orthology set included in WormBase has been updated to the latest version (13.0).

DNAseI hypersensitive Sites

We have created 42,728 Features with a Method=DNAseI_hypersensitive_site to mark DNase hypersensitivity sites found in C. elegans ’embryo’ and ‘L1 arrest’ life-stages in non-coding regions from the paper WBPaper00053259. These sites, together with Transcription Factor footprints, will be added to the tracks available in the genome browsers.

Genome Res. 2017 Dec;27(12):2108-2119. “Genome-wide discovery of active regulatory elements and transcription factor footprints in Caenorhabditis elegans using DNase-seq.”  Ho MCW, Quintero-Cadena P, Sternberg PW.

WormBase Version WS262

If you noticed, version WS262 has been out for several days.  The version number present at the top of the WormBase home page is now a link to the Release Notes which is a concise summary listing the various data types and their numbers.  Check it out if you want to get a quick view of the breadth and depth of the data in WormBase and to see what has changed since the last release.  Also find the list of data files available for this release, on our FTP site.

WormBase is updated to WS260

The 260th version of WormBase has been released!  The release notes that are published with each new release gives you various statistics about the data in the current release as well as providing a quick peak at the breath and depth of the data in WormBase.  It also lists all the data files available for download at our FTP site.  Check all of these out and let us know if you have any suggestions or questions!

WormBase release WS248

The newly released WS248 version of WormBase includes several updates based on curation topics as well as synchronisation with other databases.
In addition the use of Gene Ontology has been extended.

microRNA update for Brugia malayi

The newest data on Brugia malayi microRNAs from miRBase Release 21 has been integrated,
which includes pre-miRNA and mature transcripts as well as the consolidation of
nomenclature used by WormBase and miRBase.

Heavy Metal Topic curation

This release focuses on the curation of data related to Heavy Metal response in nematodes.
Supporting data and publications have been added to WormBase, in addition to review of
gene models for genes involved in this pathway.

New automated descriptions

Gene descriptions generated automatically using a new in-house pipeline were rolled out
for C. elegans in the WS247 release. This release extends that to all other core
species (B. malayi, O. volvulus, C. briggsae, C. brenneri, C. remanei, C. japonica)

New Gene Ontology Annotation Class

Starting with the WS248 release, Gene Ontology annotations will be represented in a new class,
GO_annotation. The GO_annotation class modelsGO annotations as distinct objects in the
database and allows for richer representation of GO data. For example, the GO_annotation
class contains information on interacting genes for annotations that use the IGI (Inferred
from Genetic Interaction) and IPI (Inferred from Physical Interaction) evidence codes, and
also contains annotation extensions that provide additional context for GO terms, such as
substrates for enzymatic activities. The GO_annotation class also includes annotations from
external groups such as UniProt and the Gene Ontology Consortium’s phylogenetic annotation
efforts using PAINT.