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

Accessing the WormBase FTP site

You may have noticed that many browsers such as Chrome, Firefox, etc., no longer support the File Transfer Protocol (FTP) to access files on remote servers. However, programs such as FileZilla offer free support of FTP. Please stay tuned as we are currently exploring solutions to make access to the WormBase FTP site easier for our users.

WormBoard Election

Dear Lab Heads, 

Please forward this email to everyone in your lab! 

Election of WormBoard members is occurring this year as described here: https://wiki.wormbase.org/index.php/WormBoard

Please go to this website:  https://forms.gle/BLGz9mhTmtxLD1vW6 and follow instructions to cast your ballot for the indicated representative slots. 

Each member of the worm community may cast one vote. 

Please forward this message to everyone in your group. 

Voting will close June 7 2021.  

Best wishes, 
Jane Hubbard (for the election committee)

Introducing Wormicloud, a text summarization tool

We are happy to introduce Wormicloud, a new tool that summarizes scientific articles in a graphical way through word clouds. This tool is aimed at facilitating the discovery of new experimental results not yet curated by model organism databases and is designed for both researchers and biocurators. Wormicloud is customized for the Caenorhabditis elegans literature and provides several advantages over existing solutions, including being able to perform full-text searches through Textpresso, which provides more accurate results than other existing literature search engines.

Wormicloud is integrated through direct links from gene interaction pages in WormBase. Additionally, it allows analysis on the gene sets obtained from literature searches with other WormBase tools such as SimpleMine and Gene Set Enrichment. URL: https://wormicloud.textpressolab.com

You can also read the paper that describes Wormicloud.

Wormicloud