Development of dictyBase, an online informatics resource

dictyBase is the manually curated model organism database (MOD) for the eukaryote Dictyostelium discoideum and related species. Dictyostelium is widely used to study of cellular processes such as cell motility, chemotaxis, signal transduction, cellular response to drugs, and host-pathogen interactions. Dictyostelium’s genome includes genes with significant homology to vertebrate, yeast and microbial genes, attracting researchers interested in a wide variety of biological topics such as human disease, comparative genomics, and self/non-self recognition. dictyBase enables researchers to view and download up-to-date genomic, functional and technical information. Teachers appreciate the wealth of available teaching materials and technological protocols. Many users consider dictyBase their most important community resource, where help from dictyBase staff (dictyBase help line) or from other users (Dicty ListServ, moderated by dictyBase) is never far away. dictyBase users benefit from its tight integration with the Dicty Stock Center. Advances in the biomedical field such as next generation sequencing and proteomic studies demand modern approaches to house and represent data. This application seeks support to continue operating and expanding this important community resource. The goals for this proposal are (1) Annotate Dictyosteliid genomes and curate experimental results from the literature for D. discoideum by (a) expert curation of published data including nomenclature, functional annotations and mutant strains and their phenotypes, as well the new data types such as expression, disease genes, and signaling pathways. All this will be accomplished using a novel, integrated curation tool; (b) community curation will be a supervised form of literature curation by authorized users, as well as gene model curation for the other Dictyosteliids, while (c) automated annotations will use D. discoideum functional and gene model annotations and automatically transfer these to orthologs in the other Dictyosteliids using the MAKER tool; (2) Improve dictyBase utility and usability by (a) implementing new tools for improving data access such as a new, versatile genome browser (JBrowse), DictyAccess, a dashboard tool representing all data comprehensively and visually, a modern guided search tool also known as ‘faceted search’, and dictyMine, an advanced search tool; and (b) modernizing the web interface by using HTML5 and CSS3 technologies and by reorganizing the contents and increasing the dynamic nature of our web presence; we will also continue to (c) support dictyBase users via personalized responses and with online tutorials and videos for our new tools; (3) Integrate, analyze and display novel data sets such as (a) protein-protein interactions, (b) post-translational modifications (c) signaling pathways, and (d) genomic variations. Implementing these improvements will deepen the annotation of D. discoideum and spread first-rate annotations to other Dictyosteliids while modernizing the infrastructure and representing the data we hold in an intuitive and state of the art web interface.