PomBase
 | |
|---|---|
| Content | |
| Description | PomBase: a Schizosaccharomyces pombe resource. |
| 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, European Bioinformatics Institute and University College London |
| Authors | Valerie Wood, Midori A Harris, Antonia Lock, Mark D McDowall, Kim Rutherford, Jurg Bahler, Paul Kersey, Steve Oliver |
| Primary citation |
Wood, et al (2012)[1] McDowall, et al (2015)[2] |
| Release date | 2011 |
| Access | |
| Website | PomBase.org |
| Download URL | FTP |
| Web service URL | Genome Browser |
| Tools | |
| Standalone | BLAST, Ensembl |
| 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.
Gene pages provide manually curated annotations using ontologies to facilitate integration with data from other species and linking between different data types. For example, Gene Ontology (GO) terms describe the functions and locations of gene products, and Sequence Ontology terms describe DNA or protein features. For phenotypes, PomBase has developed the Fission Yeast Phenotype Ontology (FYPO),[3] and supports annotations to FYPO terms with details of genotypes, alleles, expression and assay conditions as well as experimental evidence.
A genome browser displays high-throughput datasets in the context of the genome sequence. The browser and other tools facilitate viewing, querying and downloading sequence and annotation data.
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.
Usage of PomBase as a research tool is explored in its NAR Database Issue papers [1][2] and in a recently published primer on S. pombe as a model organism [5]
References
- 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. PMC 3245111
. PMID 22039153. doi:10.1093/nar/gkr853. - 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. PMC 4383888 . PMID 25361970. doi:10.1093/nar/gku1040.
- ↑ Harris MA, Lock A, Bähler J, Oliver SG, Wood V (Jul 2013). "FYPO: The Fission Yeast Phenotype Ontology.". Bioinformatics. 29 (13): 1671–8. PMC 3694669 . PMID 23658422. doi:10.1093/bioinformatics/btt266.
- ↑ 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. PMC 4058955 . PMID 24574118. doi:10.1093/bioinformatics/btu103.
- ↑ 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. PMC 4596657 . PMID 26447128. doi:10.1534/genetics.115.181503.