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–

  1. Introduction to the WormBase webpages and widgets
  2. WormBase data mining tools: SimpleMine, WormMine, BioMart
  3. WormBase ontologies and gene set enrichment analysis
  4. WormBase JBrowse: tutorial and demo
  5. Community curation
  6. 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!

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!

Come and talk to WormBase staff at the IWM 2019!

It’s that year again when worm breeders and worm lovers will be at UCLA from June 20th-24th for the International Worm Meeting. WormBase will be there in full force and will participate in several events–talks, workshops and booths. WormBase staff will be at our booth during the poster sessions in Pauley Pavilion, come talk to us and feel free to ask any questions related to data and data querying and give us your suggestions and comments. Also, take the opportunity to visit the microPublication booth and find out how to micropublish your results. WormBase related events at IWM 2019 include–

  • Thursday June 20th
    -2.30 pm-5.30pm, Northwest Auditorium:  Workshop, 4th Parasitic Nematodes: Bridging the Divide Workshop.
    -9.59 pm: At Plenary Session 1, WormBase 2019: using Artificial and Real Intelligence. Paul Sternberg, California Inst of Technology.
  • Friday, June 21st and Saturday, June 22nd
    -7.30 pm-10.30 pm, Pauley Pavilion: WormBase booth, open for questions, comments, suggestions.                                 
    -7.30 pm-10.30 pm, Pauley Pavilion: microPublication booth, come by to learn about micropublishing.
  • Saturday June 22nd
    -07:30 am-08:30 am, DeNeve Private Dining Room: microPublication Biology: How to Publish your Single Experimental Findings
    -1:00 pm-2.30 pm: Workshop, Wormbase 2019:Data, Tools, and Community Curation
  • Sunday June 23rd
    -3:00 pm-6:00 pm, Pauley Pavilion: WormBase booth, open for questions, comments, suggestions.                                 
    -3:00 pm-6:00 pm, Pauley Pavilion: microPublication booth, come by to learn about micropublishing.