Integrated Data Visualization for Bacteria in the Oralgen DB
Creators: name: University Of California Office Of The President
Publisher: name: University of California Office of the President
publisherIdentifier: https://ror.org/00dmfq477
publisherIdentifierScheme: ROR
Year: 2024

description: Publicly accessible (i.e. open) life science databases have become vital resources for successful experimental biology and biomedicine. Free web-based resources also serve as educational aids in science teaching from high school through to academia, regardless of the financial situation of the establishment. While at first genomic data consisted exclusively of DNA sequences (and inferred protein sequences) new kinds of biological data are now rapidly emerging through functional genomics initiatives and advances in biomolecular engineering (for example through the use of DNA microarrays). A database user typically has two main desires: (i) effective access to as much information as possible, (ii) quality control and annotation. A developer team is challenged to adapt the database interface to new developments when aiming to provide, and maintain, a user-friendly modern resource. One of the most effective ways to improve specialist databases is to incorporate carefully selected, suitable developments by other groups. Here we propose a small-project collaboration over 15 months between UCSC and LANL, to investigate the suitability of highly intuitive user interface designs for non-expert biologist users previously developed at UCSC, for future incorporation and use at an existing public oral bacterial pathogen database at LANL, Oralgen (www.oralgen.lanl.gov). Previous work in the PI’s group at the University of Edinburgh and UC Santa Cruz has yielded innovative data visualization tools that facilitate exploration-style analysis. Exploration-style analysis can be viewed as taking browsing of data to a next level, through (i) visual, interactive interfaces (which we call viewers); (ii) integrated (i.e. simultaneous, overlaid) display of different kinds of biological data but easy navigation; (iii) the possibility to modify the selected sets of genes of interest easily, without having to return to a search page. Our primary motivation for developing different such tools (so far, one for budding yeast (YETI: www.yetibio.com) and one for the prevalent human malarial parasite (MaGnET: www.malariagenomeexplorer.org)), is to experiment with their visual display designs and obtain feedback from the users so they can be further improved. We find that our tools are valuable to biologists when forming, and pursuing hypotheses that make non-obvious functional connections between several gene products. Ultimately, the question we are aiming to answer through this primer project is: Could a future novel user interface to the Oralgen DB incorporate graphic display designs currently featured in Gerloff group software for eukaryote functional genomic data – and if yes, which designs should be incorporated? To accomplish this one UCSC graduate student will be working together with two advisors and their teams at UCSC and LANL. S/he will pursue three specific aims: (1) Build on the design of the currently existing Exploration tools, and develop similar visual displays for data from bacterial species (the current prototypes YETI and MaGnET are for eukaryote unicellular species). (2) Develop prototype versions of the visualization software that are tailored to the oral bacterial pathogens featured in Oralgen (currently 15 species) so that the programs can be used to investigate the utility of incorporating such displays in future user interfaces to the database. (3) Evaluate, and revise/refine, the prototype versions based on user feedback. Technically work on the project is facilitated by the fact that both Oralgen and the UCSC Exploration tools store their data in MySQL databases. While Oralgen’s user interfaces are written in more common web-interface languages than Java the new bacterial exploration tools emerging from the project will be Java-based to enable easy modification of the design by the student. All developments will be freely available to the public, for use via the Internet and/or for download. This project offers a unique research and training experience for the student involved, and furthers research exchange between the UC and NL campuses. Most insights gained during this project will generally apply to bacterial species, and be transferable to further new resources for other bacteria in the future. Our research facilitates open/free access to modern biological data and information about important pathogens, which will impact on experimental design and knowledge, in both laboratories and schools, world-wide.