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!
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.
* 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
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
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.
It has become necessary for us to modify the structure of the “releases” branch FTP site. The reason for this is that we are now required to represent potentially multiple alternative reference genomes sequences for a single nematode species (e.g. Ascaris suum).
In many cases, these references will originate from different strains, but that may not always be the case. We have therefore chosen to differentiate between alternative reference genomes for a single species by including the NCBI BioProject accession (http://www.ncbi.nlm.nih.gov/bioproject) in the directory path and files names. Alternative genome sequencing efforts for the same species will each be assigned their own unique NCBI BioProject accession.