WormBase ParaSite release 2: more genomes and new data-mining tool

We are pleased to announce the second release of WormBase ParaSite, the home for parasitic worm draft genomes and genomic data in WormBase.

This release includes eight new annotated genomes, taking the total number of nematode and flatworm genomes in WormBase ParaSite to 97, representing 89 species. The new genomes include:

Fasciola hepatica (PRJEB6687)
Opisthorchis viverrini (PRJNA222628)
Pristionchus exspectatus (PRJEB6009)
* Five Steinernema genomes, including Steinernema carpocapsae (PRJNA202318)

    This release also includes a new data-mining tool, the WormBase ParaSite BioMart. The interface and underlying software for this are based on the Ensembl BioMart, the main difference being that WormBase ParaSite BioMart collects data for all species into a single underlying database. This means that a single query can be used to filter and report data from multiple species at once, for example all species of a given taxonomic clade.

    New in WS246: Automatically generated gene descriptions

    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

    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

    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

    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.