PomBase
| File:PomBase Logo.png | |
|---|---|
| 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
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