For miRNA fans

For miRNA fanatics out there, we have added 90 miRNA gene clusters from MirGeneDB to the C. elegans annotation in release WS284. This complements the 20 clusters (800 objects) which were already there, making the WormBase miRNA collection possibly the most complete in the world. You can access the miRNAs through the web pages https://wormbase.org/search/all/miRNA, or through JBrowse tracks “Curated Genes(noncoding)” e. g. And don’t forget WormBase also has an impressive collection of other non-coding RNAs as well; circRNAs, lincRNAs, piRNAs, snRNA, snoRNAs, precursors and many more. Happy investigating!

New release of the Alliance of Genome Resources

Check out the latest release (5.1.0) of the Alliance of Genome Resources for your favorite worm gene and get great comparative data across the major model organisms. A notable addition to this Alliance release are the member pages which link to organism or GO related data within the Alliance and to the model organism database or the GO Consortium. These pages can be accessed from the “Members” menu at the top of Alliance web pages. See the complete release notes for the 5.1.0 release.

Take note! Author First Pass Version 3 now in production!

WormBase is excited to announce the release of a newly updated version of Author First Pass (AFP). Based on valuable feedback from our users, we’ve made several improvements, including:

  • Acknowledge author contributions on WormBase Paper and Person pages
  • Improved accuracy of entity extraction
  • Simplified data entry and updated instructions for data submission
  • Created a link to the ‘WormBase AFP Webinar‘ video
  • Updated the FAQs

Further enhancements and details are available in the V3 Release Notes.

As always, thank you to the awesome C. elegans community for your participation and input; we look forward to seeing your future submissions!

SimpleMine Update: Biotype, GO term, RNAi clone and more

We have added new data fields to SimpleMine, a batch download tool for essential gene information. Users can now access biotype, GO term, and RNAi clones through this simple web interface.

We also added more information to previously existing data fields. All references, including books, reviews, meeting abstracts, and primary research articles, are now listed in the Reference field. For genetic map position, we display error rates of the genetic mapping data. In addition to all “live” gene objects, users can now search for pseudogene or “suppressed” gene objects. 

Changes to the web interface include: improved performance, species-specific or mixed-species searches and a search button for all genes in one species. There are 32 data fields in SimpleMine, organized into five categories so that users can quickly select them. 

Note that WormBase SimpleMine provides essential information for genes in nine nematode species. There is a prototype of the SimpleMine tool for the Alliance of Genome Resources with data related to human, mouse, rat, zebrafish, fly, yeast, and worm (C. elegans only):  https://www.alliancegenome.org/prototypes