WormMine unavailable until Friday, October 30th

Due to scheduled service windows and final preparations of an update, the old instance of WormMine will be unavailable for approximately five days.

The WormMine service will return Friday, October 30th along with the WS250 release of WormBase. In the interim, please feel free to contact us should you have specific data mining queries.

September 2015: 17 new labs have joined the community!

As part of a new series of posts exploring the C. elegans research community, we’ll periodically be announcing new labs as they join the field.

17 new labs were registered with WormBase and the CGC during the WS248 and WS249 releases of WormBase. Please join us in welcoming these labs to the community!

PI Lab Code Allele Code Institute Website
Amir Sapir AMS win University of Haifa at Oranim, Tivon, Israel lab website
Buck S. Samuel BIG sml Baylor College of Medicine, Houston, TX lab website
Brent Neumann BXN cjn Monash University, Clayton, Victoria, Australia lab website
Diana E. Libuda DLW lib University of Oregon, Eugene, OR lab website
Eric Greer EZE elg Harvard Medical School, Boston, MA lab website
Florian Steiner FAS uge University of Geneva, Geneva, Switzerland lab website
Frank Schroeder FCS asc Cornell University, Ithaca NY lab website
Kris Gunsalus GKC uae New York University, NY lab website
Takaaki Hirotsu HRT frm Kyushu University, Fukuoka, Japan
Howard Riezman HRW gva University of Geneva, Geneva, Switzerland lab website
Takeshi Adachi QE var Kanagawa University, Kanagawa, Japan
Scott Rifkin QY sar University of California, San Diego, CA lab website
Shih-Peng Chan SPN chs National Taiwan University, Taipei, Taiwan
Zhou Du SYS dev Chinese Academy of Sciences, Beijing, China
Nate Dudley TCB nat TrySci Community Biolabs, Independence, MO lab website
Peter Sarkies TEE lcs Imperial College, London, UK lab website
Taro Ogurusu TOG ogr Iwate University, Morioka, Iwate, Japan

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.