Since its creation in 2014, WormBase ParaSite (http://parasite.wormbase.org) has been serving the helminthology community by gathering, organising and presenting helminth genomes on a large scale. Aiming to interrogate data for nearly all nematode and platyhelminth genomes, we are now presenting data for 202 genomes from 163 species including all major human-infective helminths as well as many plant and animal infective species of major agricultural importance. The resource also includes free-living relatives of the parasitic helminths, providing critical insights into their evolutionary histories, host-adaptation, and invasion. WormBase ParaSite takes publicly available genomes and annotations from the European Nucleotide Archive (ENA), and uses scalable automated methods to add further value to the data by way of systematic and consistent functional annotation (e.g. repetitive elements, non-coding genes annotation, protein domains, Gene Ontology terms), and comparative analysis (e.g. orthologues and paralogues). The data is presented in a user-friendly format providing several ways to explore it including genome and gene summary pages, text search, sequence search, a query wizard, bulk downloads functionality, a choice of genome browsers, an Application Programming Interface (API) and a high-throughput expression analysis suite.
In our latest release, WBPS16 - launched in September 2021, we have developed a system for capturing and presenting published gene-phenotype associations for well-studied genomes and propagating these associations between orthologs to all our hosted species. A researcher is therefore able to view phenotypes observed for their gene of interest and/or its orthologues for every species in WormBase ParaSite. These associations have been curated from the literature over many years, from RNAi and variant data. Until today, the majority of these datasets have been for Caenorhabditis elegans. However, we have already included data from a Schistosoma mansoni study and we anticipate that more gene-phenotype association studies of this type for helminths in the future. Further recent updates also include improved assembly/annotation quality metrics reported on our genome pages, while we have also introduced an archiving service so older WormBase ParaSite releases will remain available for browsing. Driven by community demand and the availability of new datasets we supplement our in-house curation platform by hosting Web Apollo instances for an increasing number of genomes.
As ever, WormBase ParaSite looks to further improve by adapting to the rapidly evolving field of worm omics. We, therefore, encourage the community to describe your use cases and make suggestions for improvements to help us prioritise future work.
