Gene Ontology Consortium turns 20

The Gene Ontology (GO) resource turns 20! Check out the latest paper describing this resource.  WormBase uses GO to describe the molecular function, cellular localization and the biological processes that a gene is involved in.  These annotations are displayed in the Gene Ontology widget on all gene pages in WormBase.  The ontology structure including the number of genes annotated to each term can be viewed via tools such as the Ontology Browser. GO Enrichment Analysis can be performed using tools on the GO website.  Data files (known as gene association files) of all the GO annotations in the latest WormBase release (note that these are ahead of the live website) across the genome for C. elegans and several other nematode species can be found here on the WormBase FTP site.

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.