PomBase

PomBase
Content
Description The scientific resource for Schizosaccharomyces pombe
Data types
captured		 Molecular Function, Biological Process, Cellular Component, Phenotype, Genotype, Allele, Protein Modification, Gene Expression, Protein expression, Nucleotide Sequence, RNA sequence, Protein sequence, Genomics, Human Orthologs, Saccharomyces cerevisiae Orthlogs, Complementation, Disease Associations, Protein features, Physical Interactions, Genetic Interactions
Organisms Schizosaccharomyces pombe
Contact
Research center University of Cambridge and University College London
Authors Antonia Lock, Midori A Harris, Kim Rutherford, Jürg Bähler, Steve Oliver, Valerie Wood
Primary citation Wood, et al (2012)[1]
McDowall, et al (2015)[2]
Release date 2011
Access
Website PomBase.org
Download URL Downloads
Web service URL Genome Browser
Miscellaneous
License Public domain
Curation policy Professionally and community curated
Bookmarkable
entities		 Yes

PomBase is a model organism database that provides online access to the fission yeast Schizosaccharomyces pombe genome sequence and its features, together with a wide range of associated biological data and references to supporting literature.


Data Organization

An overview of data provided by PomBase and ways to access it.

PomBase provides genome-wide datasets and gene-specific annotation. Genome-wide datasets (including protein datasets, all annotations, manually curated ortholog lists etc) can be accessed from the datasets page. A genome browser (JBrowse instance) displays high-throughput datasets in the context of the genome sequence.

Gene annotation can be viewed either at a gene-specific level (on the gene pages) or at a term-specific level (on the ontology term pages). This makes it possible to either:

  • View all annotations created for gene Y
  • View all genes annotated to term X

PomBase uses several biological ontologies to capture gene-specific information, including:

  • Gene Ontology (GO) - used to describe the enzymatic functions, biological roles and cellular locations of gene products
  • Fission Yeast Phenotype Ontology (FYPO),[3] Used to associate phenotypes with alleles of genes, in comparison to the phenotype of the reference strain
  • Sequence Ontology - used to describe DNA or protein features
  • Protein modifications - using PSI-MOD

The GO slim page provides an overview of the biological role of all fission yeast genes. PomBase also maintains a list of priority genes - these are genes with orthologs in vertebrates, but where the biological role of the gene is unknown in any species, making them especially of interest for functional characterization.

Data Input

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, [4] has been developed.

Documentation

Pombase provides both documentation and an FAQ.

Usage of PomBase as a research tool is explored in the "Eukaryotic Genomic Databases" (Methods and Protocols) book chapter [5]. Developments and updates are described in the NAR Database Issue papers [1][2]. For a detailed overview of using S. pombe as a model organism see the genetics primer [6]

References

  1. 1 2 Wood V, Harris MA, McDowall MD, Rutherford K, Vaughan BW, Staines DM, Aslett M, Lock A, Bähler J, Kersey PJ, Oliver SG (Jan 2012). "PomBase: a comprehensive online resource for fission yeast". Nucleic Acids Res. 40 (Database issue): D695–9. doi:10.1093/nar/gkr853. PMC 3245111. PMID 22039153.
  2. 1 2 McDowall MD, Harris MA, Lock A, Rutherford K, Staines DM, Bähler J, Kersey PJ, Oliver SG, Wood V (Jan 2015). "PomBase 2015: updates to the fission yeast database". Nucleic Acids Res. 43 (Database issue): D656–61. doi:10.1093/nar/gku1040. PMC 4383888. PMID 25361970.
  3. ↑ Harris MA, Lock A, Bähler J, Oliver SG, Wood V (Jul 2013). "FYPO: The Fission Yeast Phenotype Ontology". Bioinformatics. 29 (13): 1671–8. doi:10.1093/bioinformatics/btt266. PMC 3694669. PMID 23658422.
  4. ↑ Rutherford KM, Harris MA, Lock A, Oliver SG, Wood V (Jun 2014). "Canto: an online tool for community literature curation". Bioinformatics. 30 (12): 1791–2. doi:10.1093/bioinformatics/btu103. PMC 4058955. PMID 24574118.
  5. ↑ Lock, A; Rutherford, K; Harris, MA; Wood, V (2018). PomBase: The Scientific Resource for Fission Yeast. Methods in Molecular Biology (Clifton, N.J.). Methods in Molecular Biology. 1757. pp. 49–68. doi:10.1007/978-1-4939-7737-6_4. ISBN 978-1-4939-7736-9. PMID 29761456.
  6. ↑ Hoffman CS, Wood V, Fantes PA (Oct 2015). "An Ancient Yeast for Young Geneticists: A Primer on the Schizosaccharomyces pombe Model System". Genetics. 201 (2): 403–23. doi:10.1534/genetics.115.181503. PMC 4596657. PMID 26447128.
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