PomBase

File:PomBase infographic.jpg

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.{{cite journal |last1=Wood |first1=V |last2=Carbon |first2=S |last3=Harris |first3=MA |last4=Lock |first4=A |last5=Engel |first5=SR |last6=Hill |first6=DP |last7=Van Auken |first7=K |last8=Attrill |first8=H |last9=Feuermann |first9=M |last10=Gaudet |first10=P |last11=Lovering |first11=RC |last12=Poux |first12=S |last13=Rutherford |first13=KM |last14=Mungall |first14=CJ |title=Term Matrix: a novel Gene Ontology annotation quality control system based on ontology term co-annotation patterns. |journal=Open Biology |date=September 2020 |volume=10 |issue=9 |pages=200149 |doi=10.1098/rsob.200149 |pmid=32875947|pmc=7536087 |doi-access=free }}

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

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 [https://www.pombase.org/gene/SPBC19C2.05 pat1]
• View all genes annotated a term, for example [https://www.pombase.org/term/GO:0000910 cytokinesis]
• View all annotations created from a specific reference, for example [https://www.pombase.org/reference/PMID 26776736 Chica et al. 2016]

Genome-wide datasets (including protein datasets, all annotations, manually curated ortholog lists etc) can be accessed from the [https://www.pombase.org/datasets datasets] page. Datasets suitable for display in a genome browser and that have been loaded can be accessed via the [https://www.pombase.org/jbrowse/?loc=I%3A1229541..1249541&tracks=PomBase%20forward%20strand%20features%2CPomBase%20reverse%20strand%20features&highlight= 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),{{cite journal|vauthors=Harris MA, Lock A, Bähler J, Oliver SG, Wood V | title = FYPO: The Fission Yeast Phenotype Ontology |journal = Bioinformatics| volume = 29| issue = 13| pages = 1671–8|date= Jul 2013| pmid = 23658422| doi = 10.1093/bioinformatics/btt266 | pmc=3694669}} 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{{cite journal |last1=Montecchi-Palazzi |first1=L |last2=Beavis |first2=R |last3=Binz |first3=PA |last4=Chalkley |first4=RJ |last5=Cottrell |first5=J |last6=Creasy |first6=D |last7=Shofstahl |first7=J |last8=Seymour |first8=SL |last9=Garavelli |first9=JS |title=The PSI-MOD community standard for representation of protein modification data. |journal=Nature Biotechnology |date=August 2008 |volume=26 |issue=8 |pages=864–6 |doi=10.1038/nbt0808-864 |pmid=18688235|s2cid=205270043 }}

The [https://www.pombase.org/browse-curation/fission-yeast-go-slim-terms 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,{{cite journal |last1=Wood |first1=V |last2=Lock |first2=A |last3=Harris |first3=MA |last4=Rutherford |first4=K |last5=Bähler |first5=J |last6=Oliver |first6=SG |title=Hidden in plain sight: what remains to be discovered in the eukaryotic proteome? |journal=Open Biology |date=28 February 2019 |volume=9 |issue=2 |pages=180241 |doi=10.1098/rsob.180241 |pmid=30938578|pmc=6395881 }} 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 [https://www.pombase.org/gene_subset/non_go_slim_without_bp_annotation uncharacterized fission yeast proteins]. The [https://www.pombase.org/status/priority-unstudied-genes 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,{{cite journal|vauthors=Rutherford KM, Harris MA, Lock A, Oliver SG, Wood V | title = Canto: an online tool for community literature curation.|journal = Bioinformatics| volume = 30| issue = 12| pages = 1791–2|date=Jun 2014| pmid = 24574118 | doi = 10.1093/bioinformatics/btu103 | pmc=4058955}} has been developed. Community curation is reviewed by PomBase staff, and this results in highly accurate, effectively co-curated, annotations.{{cite journal |last1=Lock |first1=A |last2=Harris |first2=MA |last3=Rutherford |first3=K |last4=Hayles |first4=J |last5=Wood |first5=V |title=Community curation in PomBase: enabling fission yeast experts to provide detailed, standardized, sharable annotation from research publications. |journal=Database: The Journal of Biological Databases and Curation |date=1 January 2020 |volume=2020 |doi=10.1093/database/baaa028 |pmid=32353878|pmc=7192550 }}

PomBase maintains an [https://curation.pombase.org/pombe/stats/annotation annotation stats page].

• News updates on the PomBase [https://www.pombase.org/ homepage]
• Posts to the research community [https://lists.cam.ac.uk/mailman/listinfo/ucam-pombelist mailing list]
• NAR ([Nucleic Acids Research]) database updates
• Tweets ([https://twitter.com/pombase?lang=en @PomBase])
• [https://www.facebook.com/pombase/?jazoest=26510012111665749810310311690741191091091051198050111808749509012110911956839088727611071120741057611965105565211958651001207077551119710812112285113671168799851024810370684512210256825212210910983118111111568911366104119874987103 Facebook group]
• [https://www.linkedin.com/groups/5122686/ Linkedin group]

Pombase provides both [https://www.pombase.org/documentation documentation] and an [https://www.pombase.org/faq FAQ].

Usage of PomBase as a research tool is explored in the "Eukaryotic Genomic Databases" (Methods and Protocols) book chapter.{{Cite book |last1=Lock |first1=A |last2=Rutherford |first2=K |last3=Harris |first3=MA |last4=Wood |first4=V |title=Eukaryotic Genomic Databases |chapter=PomBase: The Scientific Resource for Fission Yeast |date=2018 |volume=1757 |pages=49–68 |doi=10.1007/978-1-4939-7737-6_4 |pmid=29761456|pmc=6440643 |series=Methods in Molecular Biology |isbn=978-1-4939-7736-9 }} Developments and updates are described in the NAR Database Issue papers.{{cite journal|vauthors=Wood V, Harris MA, McDowall MD, Rutherford K, Vaughan BW, Staines DM, Aslett M, Lock A, Bähler J, Kersey PJ, Oliver SG | title = PomBase: a comprehensive online resource for fission yeast| journal = Nucleic Acids Res.| volume = 40| issue = Database issue| pages = D695–9|date=Jan 2012| pmid = 22039153 | doi = 10.1093/nar/gkr853| pmc=3245111}}{{cite journal|vauthors=McDowall MD, Harris MA, Lock A, Rutherford K, Staines DM, Bähler J, Kersey PJ, Oliver SG, Wood V | title = PomBase 2015: updates to the fission yeast database| journal = Nucleic Acids Res.| volume = 43| issue = Database issue| pages = D656–61|date=Jan 2015| pmid = 25361970 | doi = 10.1093/nar/gku1040| pmc=4383888}}

For a detailed overview of using S. pombe as a model organism see the genetics primer {{cite journal|vauthors=Hoffman CS, Wood V, Fantes PA | title = An Ancient Yeast for Young Geneticists: A Primer on the Schizosaccharomyces pombe Model System|journal = Genetics| volume = 201| issue = 2| pages = 403–23|date=Oct 2015| pmid = 26447128 | doi = 10.1534/genetics.115.181503 | pmc=4596657}}

{{reflist}}

• [http://www.pombase.org PomBase]

{{Bioinformatics}}

Category:Genetics databases

Category:Genetic engineering in the United Kingdom

Category:Medical databases in the United Kingdom

Category:Medical genetics

Category:Model organism databases

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