Development of dictyBase, an online informatics resource

Project: Research project

Project Details

Description

dictyBase is the model organism database (MOD) for the eukaryote Dictyostelium discoideum and related species. A community resource, widely supported by the research community, dictyBase contains gold standard expert literature curation of genes, functional annotations using the Gene Ontology and a wide range of genomic resources. Dictyostelium is widely used to study cellular processes such as cell motility, chemotaxis, signal transduction, cellular response to drugs, and host-pathogen interactions. Dictyostelium’s genome contains significant orthologs of vertebrate, yeast and microbial genes, attracting researchers interested in a wide variety of biological topics including human disease, multicellular differentiation and comparative genomics. dictyBase enables researchers to search, view and download up-to-date genomic, functional and technical information. Dictyostelium investigators depend on dictyBase as their primary community resource, where help from dictyBase staff (dictyBase help line) or from other users (Dicty ListServ, moderated by dictyBase) is available. We are in the final stages of deploying our completely new technology stack. By the end of this year dictyBase will be run entirely as a cloud-based application. This proposal seeks support to continue operating and expanding this important community resource. Our goals for this proposal are: (Aim 1) To continue (a) expert curation by dictyBase curators and enable (b) Community curation leveraging our strong relationship with the community. We will use additional sequence data to (c) update the AX4 reference genome sequence and (d) to improve the efficiency of curation ((i) we will deploy a tool that will import publications by identifying taxonomic mentions in the document, and (ii) adding a mechanism to copy annotations between genes or strains, reducing curator time to annotate gene or mutant families. (Aim 2) We will improve dictyBase utility and usability by implementing (a) Bulk annotation methods for importing large-scale data sets using both (i) a web interface and (ii) a script/command line method. (b) We will add 10 additional Dictyostelid genomes using automated methods to annotate them. We will improve usability by implementing a (c) concurrent blast search with a new user interface and integrate this with the JBrowse display. (Aim 3) To expand the data and increase the richness of annotations available in dictyBase we will implement mechanisms to capture, store and display: (a) additional context to GO annotations (i) using existing GO extensions and (ii) annotating and displaying biological pathways using GO CAM models; (b) integrate and display genome wide insertion mutant information for over 20 thousand insertional mutants; and (c) provide a graphical display of spatial expression data using Dictyostelium anatomy ontology terms (i) by adding a track in JBrowse for genes annotated with spatial / anatomy expression terms, and (ii) to create a graphical overview in dashboard for gene expression from all available resources including RNAseq expression. As other data sets become available we will add them to dictyBase and develop methods to display the data and make it searchable.
StatusActive
Effective start/end date9/15/19 → 8/31/21

Funding

  • National Institute of General Medical Sciences (2R01GM064426-17)

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