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PomBase 2018: User-Driven Reimplementation of the Fission Yeast Database Provides Rapid and Intuitive Access to Diverse, Interconnected Information

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PomBase 2018: User-Driven Reimplementation of the Fission Yeast Database Provides Rapid and Intuitive Access to Diverse, Interconnected Information

Antonia Lock et al. Nucleic Acids Res.

Abstract

PomBase (www.pombase.org), the model organism database for the fission yeast Schizosaccharomyces pombe, has undergone a complete redevelopment, resulting in a more fully integrated, better-performing service. The new infrastructure supports daily data updates as well as fast, efficient querying and smoother navigation within and between pages. New pages for publications and genotypes provide routes to all data curated from a single source and to all phenotypes associated with a specific genotype, respectively. For ontology-based annotations, improved displays balance comprehensive data coverage with ease of use. The default view now uses ontology structure to provide a concise, non-redundant summary that can be expanded to reveal underlying details and metadata. The phenotype annotation display also offers filtering options to allow users to focus on specific areas of interest. An instance of the JBrowse genome browser has been integrated, facilitating loading of and intuitive access to, genome-scale datasets. Taken together, the new data and pages, along with improvements in annotation display and querying, allow users to probe connections among different types of data to form a comprehensive view of fission yeast biology. The new PomBase implementation also provides a rich set of modular, reusable tools that can be deployed to create new, or enhance existing, organism-specific databases.

Figures

Figure 1.
Figure 1.
Linking GO molecular functions to substrates and GO biological processes using annotation extensions. (A) Examples from the shk1 gene page illustrate uses of annotation extensions. In the GO molecular function section, an annotation indicates that Shk1 is a protein Ser/Thr kinase and extensions identify several of its substrates. Annotations in the GO biological process section show that Shk1 regulates several different pathways, but do not capture which phosphorylated substrates are relevant to which pathways. Extensions on the protein kinase molecular function annotation connect different substrates to specific processes (the underlying relation is part_of, converted to ‘involved in’ for a more human-friendly display). For example, Shk1 phosphorylates Byr1 as part of positive regulation of the pheromone MAPK cascade (green boxes). In another context, Shk1 phosphorylates Rlc1, Rlc1 is inhibited and contractile ring contraction is negatively regulated (purple boxes). (B) A representation of a signaling pathway can be built up from a series of molecular function annotations that use extensions to identify regulated kinase substrates and the biological process context in which the functions take place.
Figure 2.
Figure 2.
Using and finding ontology term pages. (A) Ontology term page layout. The page includes term details (name, ID, definition), links to external browsers and links to PomBase pages for more general terms in the ontology. Where applicable, annotations to the term are shown in a table, with summary and detailed views as on gene pages. Term pages use ontology structure to provide the ‘parent’ links and to distinguish annotations made directly to the term from annotation to any child terms. (B) Finding term pages. The PomBase advanced search can be used to find GO, phenotype (FYPO), protein modification and disease terms. On the search results page, a hyperlink goes to the term page. Term pages can also be found by searching for a term ID using the simple search box at the top of PomBase pages, or by following links where ontology terms appear in annotation extensions.
Figure 3.
Figure 3.
Annotation views. Tables of ontology-based annotations have simplified, non-redundant summary views (top) and comprehensive views showing details (bottom). ‘Show details’ and ‘Show summary’ links toggle between the views for all annotations in the table, and ± buttons switch views for individual annotations. For GO biological process terms, the detailed view also includes a ‘view ancestry’ link to a graphical ontology view (derived from QuickGO (14)) that highlights directly annotated terms and shows their links to more general terms (green boxes).
Figure 4.
Figure 4.
The new PomBase front page. The main panels highlight recent fission yeast research, community curation and PomBase usage tips (left, center and right, respectively). The page also provides news and links to example pages and frequently used tools.

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