Check out this useful chapter ‘The Caenorhabditis elegans Transgenic Toolbox‘ by Jeremy Nance and Christian Frøkjær-Jensen in the latest issue of WormBook, GENETICS.
WormBase workshop talks at the 2019 IWM available on Youtube
Talks delivered at the WormBase workshop as part of the International C. elegans meeting at UCLA in June 2019 are now available on Youtube. Please note that these are recordings done at the workshop with external cameras and microphones, so apologies if they are not of the highest quality. They are linked from their titles below–
- Introduction to the WormBase webpages and widgets
- WormBase data mining tools: SimpleMine, WormMine, BioMart
- WormBase ontologies and gene set enrichment analysis
- WormBase JBrowse: tutorial and demo
- Community curation
- Introduction to the Alliance of Genome Resources
Looking for naming conventions and guidelines?
If you have started a new worm lab or are looking for nomenclature guidelines for genes, alleles and other genetic entities, please consult this page of our online user guide–https://wormbase.org/about/userguide/nomenclature#f1il048b3g6e2597cmdjkh–10
Different types of properly named entities (genes, alleles, strains, trangenes, etc.) in published papers are identified by text-mining and other WormBase tools and/or via manual curation. Following official nomenclature guidelines makes your data discoverable by WormBase and thus to the whole community!
If you haven’t signed up with WormBase, please consider doing so!
Several interactions with WormBase require that you have a WBPerson identification. Use this form to request one, if you don’t have one already. In addition, you can also add or update your intellectual lineage.
New and Improved Author First Pass Pipeline!
Community curation is a valuable part of WormBase. For the past ten years, C. elegans researchers have participated in our ‘Author First Pass’ pipeline using a web-based form to alert WormBase curators to entities and data types in their newly published papers.
We are very excited to announce a new and improved ‘Author First Pass’ pipeline that uses the Textpresso Central text mining system to automatically extract entities and identify data types in new C. elegans papers.
As before, corresponding authors will receive an email (Help WormBase curate your paper!) shortly after publication of their paper with a link to the new form.
But now, instead of having to enter all information de novo, authors simply need to verify the results and, if need be, modify them using simple check boxes and autocomplete menus of WormBase entities.
Links from the ‘Author First Pass’ form to select data entry forms allow for more detailed community curation, if desired.
We look forward to your participation and welcome any feedback you might have on your user experience!
Many thanks to Hannes Buelow, Simon Harvey, Hang Lu, Judith Kimble, Dayong M Wang, and Kunitoshi Yamanaka for helping to test our new form!