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Database on Schizosaccharomyces pombe From Wikipedia, the free encyclopedia
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]).
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, Manuel Lera-Ramírez, Pascal Carme, Kim Rutherford, Juan Mata, Jürg Bähler, Steve Oliver, Valerie Wood |
Primary citation | Rutherford, et al (2024)[1] |
Release date | 2011 |
Access | |
Website | pombase.org |
Download URL | Downloads |
Miscellaneous | |
License | Creative Commons Attribution 4.0 International license, GNU General Public License, MIT License |
Curation policy | Professionally and community curated |
Bookmarkable entities | Yes |
PomBase staff manually curate a wide variety of data types using both primary literature and bioinformatics sources, and numerous mechanisms are employed to ensure both syntactical and biological content validity.[3]
Types of data curated include:
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:
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:
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,[6] making it one of the great unsolved problems in biology. 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.
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,[7] has been developed. Community curation is reviewed by PomBase staff, and this results in highly accurate, effectively co-curated, annotations.[8]
PomBase maintains an annotation stats page.
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.[9] Developments and updates are described in the NAR Database Issue papers.[10][11][2] For a detailed overview of using S. pombe as a model organism see the genetics primer [12]
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