New in WS246: Automatically generated gene descriptions

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WormBase has been writing concise descriptions of genes that appear in the Overview widget of the gene page. Written in prose, these descriptions provide a quick overview of gene function. Since the process of manually writing gene descriptions is a relatively slow process, many genes lacked such descriptions.

A new experimental tool at WormBase aims to fill these gaps by automatically creating gene descriptions which are visible in the Overview widget of gene pages.  The semi-automated process of generating these descriptions relies on pre-existing orthology and Gene Ontology annotations (biological process, molecular function, and cellular component) in WormBase.  This process offers a broad coverage for genes lacking manually drafted descriptions.

New Features for WS246

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Human Disease Data Update

As part of WormBase efforts to curate genes that are potential models for inherited human diseases, 867 genes have been predicted as potential disease genes. In addition curation efforts added publications on experiments using C.elegans genes to investigate human genetic diseases to 181 genes. And 244 genes have been identified from publications as being relevant to research in that field.

WormBase curates human disease relevance data by designating genes as ‘Experimental models’ for a specific human disease based on experimental data published in the literature. In addition to manual curation, an automated data pipeline designates genes as ‘Potential models’ based on orthology with the human gene. Detailed text descriptions called ‘Human disease relevance’ descriptions describe how the elegans gene is a genetic model for the human disease. All human disease relevant data can be found in the ‘Human Diseases’ widget and in the ‘Overview’ section on gene pages.

Update of Meloydogyne incognita

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The new WormBase release of WS243 will include an update to the Meloidogyne incognita assembly, which is based on scaffolding the original data published in 2008.
It will be available from the M.incognita section of the WormBase FTP site, as well as from a Genome Browser and as orthologs from already existing gene pages.

Users wishing use M. incognita data obtained from WormBase in publication should cite the following:

Abad P et al. Genome sequence of the metazoan plant-parasitic nematode Meloidogyne incognita. Nat Biotechnol. 2008 Aug;26(8):909-15.

Topic Curation – Protein Unfolding Response

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Based on feedback from the nematode community, WormBase will do a themed release for WS241, which will focus on the curation of protein unfolding response processes.

This will include new publications, ontologies, interactions, gene models and more.

During the course of the curation effort, 412 genes of C.elegans / C.remanei / C.briggsae / C.japonica / C.brenneri and B.malayi have been investigated.

Check out the data querying templates in WormMine!

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Recently, we released WormMine (available from the ‘Tools’ drop-down menu on WormBase), a data-mining tool of WormBase data. Be sure to check out the templates that we have created. Templates are ready-made queries useful for learning how to construct your own queries. To find them, look for the “Templates” tab at the top of WormMine next to the “Home” tab. Please note that this is a beta version of the tool that contains a subset of WormBase data. Later this year, WormMine will replace our previous data mining tool, WormMart.