We’ve posted presentations from the WormBase workshops at last week’s International Meeting.
WormBase HUBs
As shown during the WormBase Workshops of the International Worm Meeting 2015 at UCLA:
(Slides/Notes of the WormBase ParaSite / HUBs section)
To enable use of up to date data on external sites, WormBase is providing with each release (starting with WS248), selected annotations and comparative tracks as assembly hubs.
there are currently two types of hubs,
the UCSC version:
and a version compatible with Ensembl Genomes (future WormBase ParaSite , Ensembl and BioDalliance releases)
(production HUBs are in synch with the current live WormBase release)
Introductory chapter added to WormBook
Dear WormBook reader,
We are very happy to announce that A Transparent Window into Biology: A Primer on Caenorhabditis elegans, by Ann Corsi, Bruce Wightman, and Marty Chalfie, has just been added to WormBook as a co-publication with GENETICS. This concise and comprehensive review, which serves as an introductory chapter to WormBook, discusses the basic biology, genetics, anatomy, genomics, ecology, and evolution of C. elegans. Key discoveries resulting from research using this organism are described, as is the strong collaborative nature of the worm community. We expect this introduction to provide an invaluable resource for students and others new to C. elegans research and literature.
We thank Tracey DePellegrin, Ruth Isaacson, and Elizabeth De Stasio of GENETICS for their dedication to this collaboration, as well as Editor-in-Chief Mark Johnston for his support of the project.
Please proceed to read this new chapter and others on nematode biology at http://www.wormbook.org/. If you have any comments or suggestions, please submit them via the Feedback page on wormbook.org.
Jane
Nuclear receptor chapter updated in WormBook
Nuclear receptor signal transduction in C. elegans, by Adam Antebi, has just been published in the Signal transduction section of WormBook. This chapter updates his 2006 chapter, Nuclear hormone receptors in C. elegans. The updated chapter discusses the role of nuclear receptors as regulators of life history, cell fate, and organogenesis, and their function in nutrient sensing, metabolism and energy homeostasis.
Please proceed to read this new chapter and others on nematode biology at http://www.wormbook.org/. If you have any comments or suggestions, please submit them via the Feedback page on wormbook.org.
Thank you for your interest in WormBook.
Jane
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.