PomBase 2018: user-driven reimplementation of the fission yeast database provides rapid and intuitive access to diverse, interconnected information
Top Cited Papers
Open Access
- 13 October 2018
- journal article
- research article
- Published by Oxford University Press (OUP) in Nucleic Acids Research
- Vol. 47 (D1), D821-D827
- https://doi.org/10.1093/nar/gky961
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.Keywords
Funding Information
- Wellcome Trust (104967/Z/14/Z)
This publication has 25 references indexed in Scilit:
- A method for increasing expressivity of Gene Ontology annotations using a compositional approachBMC Bioinformatics, 2014
- Canto: an online tool for community literature curationBioinformatics, 2014
- Analysis of stress-induced duplex destabilization (SIDD) properties of replication origins, genes and intergenes in the fission yeast, Schizosaccharomyces pombeBMC Research Notes, 2012
- PomBase: a comprehensive online resource for fission yeastNucleic Acids Research, 2011
- Phylogenetic-based propagation of functional annotations within the Gene Ontology consortiumBriefings in Bioinformatics, 2011
- QuickGO: a web-based tool for Gene Ontology searchingBioinformatics, 2009
- JBrowse: A next-generation genome browserGenome Research, 2009
- The GOA database in 2009--an integrated Gene Ontology Annotation resourceNucleic Acids Research, 2009
- Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolutionNature, 2008
- A Chado case study: an ontology-based modular schema for representing genome-associated biological informationBioinformatics, 2007