PomBase


PomBase is a model organism database that provides online access to the fission yeast Schizosaccharomyces pombe genome sequence and annotated features, together with a wide range of manually curated functional gene-specific data. The PomBase website was redeveloped in 2016 to provide users with a more fully integrated, better-performing service.

Data curation

PomBase staff manually curate a wide variety of data using primary literature and bioinformatics. Types of data curated include:
Gene annotation can be viewed either at a gene-specific level or at a term-specific level. This makes it possible to either:
Genome-wide datasets can be accessed from the page. Datasets suitable for display in a genome browser and that have been loaded can be accessed via the .
PomBase uses several biological ontologies to capture gene-specific information, including:
The provides an overview of the "biological role" of all "known" fission yeast genes - these are proteins that have either been experimentally characterized in fission yeast, or in another species and transferred by orthology.
Remarkably, nearly 20% of eukaryotic proteomes, from yeast to human, are uncharacterized in terms of the pathways and processes that these proteins participate in. The role that these proteins play in biology, have not yet been discovered in any species. To aid research into these unknown proteins, PomBase maintains an inventory of . The list represents the subset of uncharacterized fission yeast genes that are conserved to man, making it an especially high priority research target.

Community co-Curation

To supplement the work of the small team of professional PomBase curators, fission yeast researchers contribute annotations directly to PomBase via an innovative community curation scheme, for which an online curation tool, Canto, has been developed. Community curation is reviewed by PomBase staff, and this results in highly accurate, effectively co-curated, annotations.
PomBase maintains an .

Knowledgebase Updates

Pombase provides both and an .
Usage of PomBase as a research tool is explored in the "Eukaryotic Genomic Databases" book chapter. Developments and updates are described in the NAR Database Issue papers.
For a detailed overview of using S. pombe as a model organism see the genetics primer