New Textpresso for OMIM!

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.


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

ParaSite Release 3

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 (, and an improved BLAST search which is faster and has no limit on the number of species that can be BLASTed against (

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!