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.

New VC2010 and improved CB4856 genomes published

The VC2010 genome assembly has just been published in Genome Research as an open-access article. This assembly is largely derived from a completely isogenic VC2010-derived strain, PD1074, that is now available from the CGC.

In related news, Junho Lee and his lab have simultaneously published an open-access article on their substantially improved genome assembly for Hawaiian C. elegans (CB4856).

UC Davis features micropublications

microPublication.org publishes brief, novel findings, negative and/or reproduced results, and results which may lack a broader scientific narrative. Each article is peer reviewed and assigned a DOI. Included data is curated and, upon publication, deposited in third party referential databases (when available).

Recently UC Davis featured an article, ‘Small Science Snippets: Micropubs Help Share Discoveries‘ about how one of their researchers used a micropublication to publish their results.

Micropublish your results today!

WormBase updated to the WS270 release

Alliance orthologs

Starting from WS270 we are using the Alliance of Genome Resources for orthologs between model organism genes. This should be more comprehensive and include the latest data from our sister databases.

VC2010 genome

An assembly and geneset of the VC2010 C.elegans strain has been added and work is ongoing to improve the integration and display of strain specific data. Additionally more mappings of N2 annotation will be included in future releases.