Biology:PomBase
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| 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 centre | University of Cambridge and University College London |
| Author(s) | Antonia Lock, Midori A Harris, Kim Rutherford, Jürg Bähler, Steve Oliver, Valerie Wood |
| Primary citation | Lock, et al (2018) [1] |
| Release date | 2011 |
| Access | |
| Website | PomBase.org |
| Download URL | Downloads |
| Web service URL | Genome Browser |
| Miscellaneous | |
| Software 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 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 (described in [2]).
Data curation
PomBase staff manually curate a wide variety of data using primary literature and bioinformatics. Types of data curated include:
- Genome sequence and features (e.g. physical location of genes in the genome)
- Protein and ncRNA functions, the cellular processes they participate in and where they localize
- Phenotypes associated with different alleles and genotypes
- Specific protein modification sites and when they occur
- Human and budding yeast orthologs of S. pombe genes (manually curated dataset)
- Metadata of datasets loaded into the genome browser
- Disease associations for when the human ortholog is known to cause disease
- Data regarding when specific genes are expressed
- Complementation data for where there is functional complementation between a fission yeast gene and a gene from another organism
- Subunit composition of complexes
Data Organization
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 a gene, for example pat1
- View all genes annotated a term, for example cytokinesis
- View all annotations created from a specific reference, for example Chica et al. 2016
Genome-wide datasets (including protein datasets, all annotations, manually curated ortholog lists etc) can be accessed from the datasets page. Datasets suitable for display in a genome browser and that have been loaded can be accessed via the PomBase JBrowse instance.
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
Gene Characterization Status
The GO slim page 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 [4]. 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 uncharacterized fission yeast proteins. The priority unstudied genes 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,[5] has been developed. Community curation is reviewed by PomBase staff, and this results in highly accurate, effectively co-curated, annotations.
PomBase maintains an annotation stats page.
Knowledgebase Updates
- News updates on the PomBase homepage
- Posts to the research community mailing list
- NAR ([Nucleic Acids Research]) database updates
- Tweets (@PomBase)
- Facebook group
- Linkedin group
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.[6] Developments and updates are described in the NAR Database Issue papers.[7][8] [9]
For a detailed overview of using S. pombe as a model organism see the genetics primer [10]
References
- ↑ Lock, A; Rutherford, K; Harris, MA; Hayles, J; Oliver, SG; Bähler, J; Wood, V (13 October 2018). "PomBase 2018: user-driven reimplementation of the fission yeast database provides rapid and intuitive access to diverse, interconnected information.". Nucleic Acids Research 47 (D1): D821–D827. doi:10.1093/nar/gky961. PMID 30321395.
- ↑ Lock, A; Rutherford, K; Harris, MA; Hayles, J; Oliver, SG; Bähler, J; Wood, V (13 October 2018). "PomBase 2018: user-driven reimplementation of the fission yeast database provides rapid and intuitive access to diverse, interconnected information.". Nucleic Acids Research 47 (D1): D821–D827. doi:10.1093/nar/gky961. PMID 30321395.
- ↑ "FYPO: The Fission Yeast Phenotype Ontology". Bioinformatics 29 (13): 1671–8. Jul 2013. doi:10.1093/bioinformatics/btt266. PMID 23658422.
- ↑ Wood, V; Lock, A; Harris, MA; Rutherford, K; Bähler, J; Oliver, SG (28 February 2019). "Hidden in plain sight: what remains to be discovered in the eukaryotic proteome?". Open Biology 9 (2): 180241. doi:10.1098/rsob.180241. PMID 30938578.
- ↑ "Canto: an online tool for community literature curation.". Bioinformatics 30 (12): 1791–2. Jun 2014. doi:10.1093/bioinformatics/btu103. PMID 24574118.
- ↑ Lock, A; Rutherford, K; Harris, MA; Wood, V (2018). PomBase: The Scientific Resource for Fission Yeast. Methods in Molecular Biology. 1757. pp. 49–68. doi:10.1007/978-1-4939-7737-6_4. ISBN 978-1-4939-7736-9.
- ↑ "PomBase: a comprehensive online resource for fission yeast". Nucleic Acids Res. 40 (Database issue): D695–9. Jan 2012. doi:10.1093/nar/gkr853. PMID 22039153.
- ↑ "PomBase 2015: updates to the fission yeast database". Nucleic Acids Res. 43 (Database issue): D656–61. Jan 2015. doi:10.1093/nar/gku1040. PMID 25361970.
- ↑ Lock, A; Rutherford, K; Harris, MA; Hayles, J; Oliver, SG; Bähler, J; Wood, V (13 October 2018). "PomBase 2018: user-driven reimplementation of the fission yeast database provides rapid and intuitive access to diverse, interconnected information.". Nucleic Acids Research 47 (D1): D821–D827. doi:10.1093/nar/gky961. PMID 30321395.
- ↑ "An Ancient Yeast for Young Geneticists: A Primer on the Schizosaccharomyces pombe Model System". Genetics 201 (2): 403–23. Oct 2015. doi:10.1534/genetics.115.181503. PMID 26447128.
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