Introducing Wormicloud, a text summarization tool

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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

Change to disease statements in gene descriptions for WS279

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Due to non-stringent human ortholog(s) and their associated diseases, C. elegans gene descriptions (displayed in the “Overview widget” of gene pages) often had spurious diseases associated with their human orthologs. With WS279, we imposed a stringency filter and only those disease associations to ortholog(s) called by more than one orthology prediction method are included in the gene description. This change has improved the accuracy of statements that read “human orthologs of this gene are implicated in <disease(s)>”. However, please note that this change has also resulted in the loss of such statements for several hundred gene descriptions due to the increased stringency.

Overview of WormBase, Sept 2020

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If you’d like to get an overview of WormBase datatypes, tools, the Author First Pass form and learn about Micropublication Biology, please take a look at the slides from a talk given by Chris Grove, a WormBase curator. This was presented at the Boston area worm meeting on Sept 23rd, 2020.