A biocurator position is open at WormBase. If you are interested and for further details please contact Paul Sternberg at pws@caltech.edu
Integrated model organism data at the Alliance of Genome Resources
It is now possible to view integrated data from six different Model Organism Databases (MODs) and the Gene Ontology (GO) Consortium at the Alliance of Genome Resources (Alliance). One can view gene descriptions, disease model data, orthology data, gene expression data and much more for the six major model organisms (yeast, worm, fly, zebrafish, mouse, rat) as well as human data on gene pages at the Alliance. You can search by gene, disease or a GO term and be taken to a page where you will find integrated views of data relevant to all of the above mentioned organisms. For example, searching by a human disease name at the Alliance will take you to a disease page where you can find data related to disease models from the six organisms. Similar integrated views are also available for orthology data for any given gene on a gene page. The Alliance is a work in progress and will host even more data in the days to come. Check it out!
New gene descriptions for the WS268 release of WormBase
The WS268 release of WormBase features new automated gene descriptions (displayed in the ‘Overview’ widget at the top of the gene page). In addition to the code being entirely rewritten, we have also added gene descriptions for a new worm species – Trichuris muris. These automated gene descriptions are highly structured and are based on curated data such as orthology data, Gene Ontology (GO) annotations, Disease Ontology (DO) annotations, gene expression data, etc., in WormBase.
The following data-types are included in the description of a given gene, when available: orthology to human genes, molecular function, biological processes, sub-cellular localization and tissue expression. A new addition to the gene descriptions is human disease relevance data in cases where the gene is used experimentally to study a disease or if it’s human orthologs are implicated in a disease.
Data content changes: For lesser known, data-poor genes, we’ve included:
1. protein domain data
2. Orthologous human gene function data drawn from the Alliance of Genome Resources.
3. Perturbation by other genes and/or chemicals and tissue enrichment data based on large scale data such as microarray, tiling arrays and RNA seq data.
Data display changes: The ‘Overview’ widget now displays only the automated gene description, however our legacy manual gene descriptions (when they do exist for genes) are collapsed but available for viewing.
Note that while the automated gene descriptions are not generated directly from the literature, most of the annotations on which they are based are manually curated from the primary literature by WormBase curators.
WormBase updated to the WS268 release
Please note that the WormBase website has been updated to the WS268 release. Details about this release may be found in the Release Notes for WS268. The notes include a list of files that we publish on our FTP site.
New chapter of WormBook in GENETICS
Check out the new chapter of WormBook in GENETICS about mitotic cell division by Lionel Pintard and Bruce Bowerman – ‘Mitotic Cell Division in Caenorhabditis elegans‘.