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Review
, 1757, 49-68

PomBase: The Scientific Resource for Fission Yeast

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Review

PomBase: The Scientific Resource for Fission Yeast

Antonia Lock et al. Methods Mol Biol.

Abstract

The fission yeast Schizosaccharomyces pombe has become well established as a model species for studying conserved cell-level biological processes, especially the mechanics and regulation of cell division. PomBase integrates the S. pombe genome sequence with traditional genetic, molecular, and cell biological experimental data as well as the growing body of large datasets generated by emerging high-throughput methods. This chapter provides insight into the curation philosophy and data organization at PomBase, and provides a guide to using PomBase for infrequent visitors and anyone considering exploring S. pombe in their research.

Keywords: Annotation extensions; Biological database; Fission yeast; GO slim; Gene ontology; Model organism; Schizosaccharomyces pombe.

Figures

Fig. 1
Fig. 1
The quick-links menu. The menu displayed on the left-hand side of gene pages provides an overview of the different data types available for specific genes, and enables rapid navigation between the different sections of the gene page
Fig. 2
Fig. 2
GO annotations and extensions. (A) Summary view of selected annotations on the clp1 gene page. The orange boxes highlight annotations representing Clp1’s roles: Clp1 dephosphorylates the Nsk1 protein to positively regulate spindle attachment to the kinetochore. During anaphase, it dephosphorylates Mde4 to positively regulate spindle elongation. Clp1 also directly targets itself during telophase to promote mitotic exit. Processes linked to molecular functions are also shown in the biological process section. Biological process annotations that map to the PomBase GO slim are shown at the top of the biological process section Fig. 2 (continued) (purple box). (B) Relations used in GO annotation extensions, showing how each links one gene to other genes or additional ontology terms, with examples for each GO branch
Fig. 3
Fig. 3
The PomBase phenotype display. (A) Summary view (B) Detailed view of a subset of phenotypes associated with alleles of cdc2. In the summary view, redundant annotations (including annotation to the same phenotype term, but with different extensions or metadata) and metadata are hidden. The detailed view shows all annotations, plus the cited references, evidence, extensions indicating penetrance, expressivity, or affected gene products, and any curated experimental, conditions. Genotype details, including the type of mutation for each allele, expression level of the gene products, and any background genotype information, are provided in a mouse-over (shown in A, orange box). A drop-down menu enables filtering for subsets of phenotypes (shown in A, green box)
Fig. 4
Fig. 4
Genotype pages. Each genotype page displays allele and expression details and all annotations associated with the genotype. In this example, the double mutant comprising cdc25-22 (C532Y) and wee1-50, both at reduced expression levels, in the background pap1::kanr bfr1::hygr pmd1::natr caf5::kanr mfs1::natr has been associated with four different phenotype terms
Fig. 5
Fig. 5
The mde4 “Target of” section. Because cdc2 is annotated to a protein kinase molecular function term, with Mde4 specified as a substrate, cdc2 is listed in the “target of” section for mde4. Reciprocal annotations are also generated from phenotype and protein modification annotations. For example, a mutation in cdc2 has an effect on mde4, with phenotypic details available on the cdc2 gene page, and a “target of” annotation using the “affected by mutation in” relationship on the mde4 gene page
Fig. 6
Fig. 6
cdc2 function–process links and downstream signaling cascades. (A) Showing the subset of Cdc2 phosphorylation targets with function–process links. Biological processes that the enzyme–substrate interaction is part of, or happens during, are indicated using the “involved in” and “during” annotation extension relationships. (B) Targets downstream of Cdc2 can be accessed via the hyperlinked annotation extension substrates, enabling users to follow biological pathways. The capturing of targets makes it possible to reconstruct pathways for a systems level representation of gene networks
Fig. 7
Fig. 7
Ontology term pages. (A) The top of the page shows the term name, ID, and definition, along with immediate parent terms. Links to external resources are provided. (B) The summary view shows genes annotated directly to the term or to any of its child terms, and includes extensions. (C) The detailed view provides additional information such as the relationship of child terms to the parent term, evidence codes and references
Fig. 8
Fig. 8
Publication pages. The PMID:25987607 page shows publication details and a community curator acknowledgement at the top, and annotations derived from the paper. GO and FYPO annotations have summary and detailed views as on gene and ontology term pages
Fig. 9
Fig. 9
Query builder filtering. (A) A list of the different filters available to identify genes of interest. (B) The history section can be used to review previously run queries. Queries can be combined using the union, intersect and subtract operators. (C) An example of the results of running and combining queries. 753 genes (August 2017) are annotated to the GO term mitochondrion. Of these, 3498 are conserved in metazoa, 595 genes where any type of allele has been associated with hydroxyuruea sensitivity and 411 genes with the characterization status “conserved unknown,” i.e., of unknown function but conserved in other organisms. The union of these four queries identifies one gene

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References

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