Genomes for the entomopathogenic nematode Steinernema carpocapsae and four congeners–S. scapterisci, S. monticolum, S. feltiae, and S. glaseri are now available in WormBase Parasite. Check out the paper describing these genomes.
The Textpresso project serves the biomedical research community by providing full text searches of the C. elegans published literature, as well as other model organism literatures. Recently Textpresso for Online Mendelian Inheritance in Man (OMIM), was developed, this contains approximately 25,000 entries from OMIM. The entries are separated into their various fields: eg., clinical synopsis (CS), number (NO), references (RF), creation date (CD), etc. One can use Textpresso search capabilities to search for various diseases, genes, etc. within OMIM entries. An intersection of these searches can be created with various categories that are integrated as part of Textpresso, for a more refined targeted search. Those categories are: gene ontology (GO), sequence ontology (SO), human anatomy (UBERON) and human phenotype ontology (HPO). Entries are downloaded from the OMIM website and updated for Textpresso weekly.
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|
We have updated WormBase to the newest version of the website and database, WS249.
You can find the release notes here.
We are pleased to announce the third release of WormBase ParaSite, the home for parasitic worm draft genomes and genomic data in WormBase.
This release includes two new annotated genomes, taking the total number of nematode and flatworm genomes in WormBase ParaSite to 99, representing 90 species. The new genomes are:
- Echinococcus canadensis (PRJEB8992)
- Loa loa (PRJNA246086)
This release also includes a REST API, providing language-neutral programmatic access to ParaSite data via a RESTful interface (http://parasite.wormbase.org/api/), and an improved BLAST search which is faster and has no limit on the number of species that can be BLASTed against (http://parasite.wormbase.org/Tools/Blast).
Finally, in this release we are displaying tapeworm RNASeq data for the species Echinococcus granulosus, Echinococcus multilocularis and Hymenolepis microstoma (as example). We will be including more transcriptomic data sets in upcoming ParaSite releases so if you would like to suggest datasets you would like to see displayed please get in touch!