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.

WormBase release WS247

Orthology update

* Data from Inparanoid was updated to version 8
* Orthology data for all core nemtatodes and model organisms was imported from WormBase Parasite release 1
* OMA and TreeFam data was removed in preparation for an update (TreeFam accessions will remain as database crossreferences)

Expression and Picture update

* A large set of expression graphs for other nematodes produced by Yanai’s has been added

RNASeq data

The RNASeq data will become richer in WS247.

There will also be “control” mean and median FPKM values derived from the data which does not have a specific experimental condition applied.

New/updated reference genomes

This release we see a rebuild of C. elegans, B. malayi and O. volvulus. Various data classes and curational activites have been undertaken on these species since the release of WS246

WormBase ParaSite release 2: more genomes and new data-mining tool

We are pleased to announce the second release of WormBase ParaSite, the home for parasitic worm draft genomes and genomic data in WormBase.

This release includes eight new annotated genomes, taking the total number of nematode and flatworm genomes in WormBase ParaSite to 97, representing 89 species. The new genomes include:

Fasciola hepatica (PRJEB6687)
Opisthorchis viverrini (PRJNA222628)
Pristionchus exspectatus (PRJEB6009)
* Five Steinernema genomes, including Steinernema carpocapsae (PRJNA202318)

    This release also includes a new data-mining tool, the WormBase ParaSite BioMart. The interface and underlying software for this are based on the Ensembl BioMart, the main difference being that WormBase ParaSite BioMart collects data for all species into a single underlying database. This means that a single query can be used to filter and report data from multiple species at once, for example all species of a given taxonomic clade.

    New in WS246: Automatically generated gene descriptions

    WormBase has been writing concise descriptions of genes that appear in the Overview widget of the gene page. Written in prose, these descriptions provide a quick overview of gene function. Since the process of manually writing gene descriptions is a relatively slow process, many genes lacked such descriptions.

    A new experimental tool at WormBase aims to fill these gaps by automatically creating gene descriptions which are visible in the Overview widget of gene pages.  The semi-automated process of generating these descriptions relies on pre-existing orthology and Gene Ontology annotations (biological process, molecular function, and cellular component) in WormBase.  This process offers a broad coverage for genes lacking manually drafted descriptions.

    New Features for WS246

    Human Disease Data Update

    As part of WormBase efforts to curate genes that are potential models for inherited human diseases, 867 genes have been predicted as potential disease genes. In addition curation efforts added publications on experiments using C.elegans genes to investigate human genetic diseases to 181 genes. And 244 genes have been identified from publications as being relevant to research in that field.

    WormBase curates human disease relevance data by designating genes as ‘Experimental models’ for a specific human disease based on experimental data published in the literature. In addition to manual curation, an automated data pipeline designates genes as ‘Potential models’ based on orthology with the human gene. Detailed text descriptions called ‘Human disease relevance’ descriptions describe how the elegans gene is a genetic model for the human disease. All human disease relevant data can be found in the ‘Human Diseases’ widget and in the ‘Overview’ section on gene pages.