PomBase is a

model organism database Model organism databases (MODs) are biological databases, or knowledgebases, dedicated to the provision of in-depth biological data for intensively studied model organisms A model organism is a non-human species that is extensively studied ...

that provides online access to the fission yeast

Schizosaccharomyces pombe ''Schizosaccharomyces pombe'', also called "fission yeast", is a species of yeast used in traditional brewing and as a model organism in molecular and cell biology. It is a unicellular eukaryote, whose cells are rod-shaped. Cells typically meas ...

genome A genome is all the genetic information of an organism. It consists of nucleotide sequences of DNA (or RNA in RNA viruses). The nuclear genome includes protein-coding genes and non-coding genes, other functional regions of the genome such as ...

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 ).

Data Curation and Quality Control

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. 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 An allele is a variant of the sequence of nucleotides at a particular location, or locus, on a DNA molecule. Alleles can differ at a single position through single nucleotide polymorphisms (SNP), but they can also have insertions and deletions ...

and

genotypes The genotype of an organism is its complete set of genetic material. Genotype can also be used to refer to the alleles or variants an individual carries in a particular gene or genetic location. The number of alleles an individual can have in a ...

* Specific protein modification sites and when they occur * Human and budding yeast

orthologs Sequence homology is the biological homology between DNA, RNA, or protein sequences, defined in terms of shared ancestry in the evolutionary history of life. Two segments of DNA can have shared ancestry because of three phenomena: either a spec ...

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 exampl
pat1
* View all genes annotated a term, for exampl
cytokinesis
* View all annotations created from a specific reference, for exampl
26776736 ''Chica et al. 2016''
Genome-wide datasets (including protein datasets, all annotations, manually curated ortholog lists etc) can be accessed from th
datasets
page. Datasets suitable for display in a genome browser and that have been loaded can be accessed via th
PomBase JBrowse instance
PomBase uses several biological ontologies to capture gene-specific information, including: *

Gene Ontology The Gene Ontology (GO) is a major bioinformatics initiative to unify the representation of gene and gene product attributes across all species. More specifically, the project aims to: 1) maintain and develop its controlled vocabulary of gene and ...

(GO) - used to describe the enzymatic functions,

biological Biology is the scientific study of life and living organisms. It is a broad natural science that encompasses a wide range of fields and unifying principles that explain the structure, function, growth, origin, evolution, and distribution of ...

roles and cellular locations of gene products * Fission Yeast Phenotype Ontology (FYPO), 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

Th
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, 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 o
uncharacterized fission yeast proteins
Th
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, has been developed. Community curation is reviewed by PomBase staff, and this results in highly accurate, effectively co-curated, annotations. PomBase maintains a
annotation stats page

Knowledgebase Updates

* News updates on the PomBas
homepage
* Posts to the research communit
mailing list
* NAR ( ucleic Acids Research database updates * Tweets
@PomBase

Facebook group

Linkedin group

Documentation

Pombase provides bot
documentation
and a
FAQ
Usage of PomBase as a research tool is explored in the "Eukaryotic Genomic Databases" (Methods and Protocols) book chapter. Developments and updates are described in the NAR Database Issue papers. For a detailed overview of using S. pombe as a

model organism A model organism is a non-human species that is extensively studied to understand particular biological phenomena, with the expectation that discoveries made in the model organism will provide insight into the workings of other organisms. Mo ...

see the genetics primer

References

External links

PomBase
{{Bioinformatics Genetics databases Genetic engineering in the United Kingdom Medical databases in the United Kingdom Medical genetics Model organism databases Science and technology in Cambridgeshire South Cambridgeshire District Wellcome Trust