WormBase 2016: expanding to enable helminth genomic research

Abstract

WormBase (www.wormbase.org) is a central repository for research data on the biology, genetics and genomics of Caenorhabditis elegans and other nematodes. The project has evolved from its original remit to collect and integrate all data for a single species, and now extends to numerous nematodes, ranging from evolutionary comparators of C. elegans to parasitic species that threaten plant, animal and human health. Research activity using C. elegans as a model system is as vibrant as ever, and we have created new tools for community curation in response to the ever-increasing volume and complexity of data. To better allow users to navigate their way through these data, we have made a number of improvements to our main website, including new tools for browsing genomic features and ontology annotations. Finally, we have developed a new portal for parasitic worm genomes. WormBase ParaSite (parasite.wormbase.org) contains all publicly available nematode and platyhelminth annotated genome sequences, and is designed specifically to support helminth genomic research.

Figure 1.

Querying multiple species in the WormBase ParaSite BioMart. A taxonomy-tree-based widget allows the selection of whole clades of species for querying, with an auto-complete feature allowing rapid identification of specific species or clades within the tree. The selection of species belonging to the Filarioidea nematode superfamily is shown.

Figure 2.

The WormBase Ontology Browser. (A) view of the anatomy term ‘mechanosensory neuron’. The sub-graph of the term and its ancestors in the hierarchy are depicted graphically to the left. To the right, the inference tree view of the term is shown, with icons indicating relationships in reference to the focus term (P = Part-of, I = Is-a). Numbers to the right are counts of genes annotated with that term (either directly or by inheritance). A list of parallel (sibling) terms to the focus term can also be viewed (bottom right). (B) main entry page for the ontology browser, which allows top-down navigation from the root term for each WormBase ontology.