PomBase

PomBase is a model organism database that provides

online access to the fission yeast Schizosaccharomyces PomBase
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 [1]). Content
Description The scientific resource
Data Curation and Quality Control for
Schizosaccharomyces
PomBase staff manually curate a wide variety of data pombe
types using both primary literature and bioinformatics Data types Molecular Function,
sources, and numerous mechanisms are employed to captured Biological Process,
ensure both syntactical and biological content validity.[2] Cellular Component,
Types of data curated include: Phenotype, Genotype,
Allele, Protein
Genome sequence and features (e.g. physical Modification, Gene
location of genes in the genome) Expression, Protein
Protein and ncRNA functions, the cellular expression, Nucleotide
processes they participate in and where they Sequence, RNA
localize
sequence, Protein
Phenotypes associated with different alleles and sequence, Genomics,
genotypes
Human Orthologs,
Specific protein modification sites and when they
Saccharomyces
occur
cerevisiae Orthlogs,
Human and budding yeast orthologs of S.
pombe genes (manually curated dataset) Complementation,
Metadata of datasets loaded into the genome Disease Associations,
browser Protein features,
Disease associations for when the human Physical Interactions,
ortholog is known to cause disease Genetic Interactions
Data regarding when specific genes are Organisms Schizosaccharomyces
expressed pombe
Complementation data for where there is
Contact
functional complementation between a fission
yeast gene and a gene from another organism Research center University of Cambridge
Subunit composition of complexes and University College
London

Data Organization Authors Antonia Lock, Midori A

Harris, Kim Rutherford,
Jürg Bähler (http://bahle
rweb.cs.ucl.ac.uk/),
Gene annotation can be viewed either at a gene-specific Steve Oliver, Valerie
level (on the gene pages) or at a term-specific level (on the Wood
ontology term pages). This makes it possible to either: [1]
Primary citation Lock, et al (2018)
View all annotations created for a gene, for Release date 2011
example pat1 (https://www.pombase.org/gene/S Access
PBC19C2.05)
View all genes annotated a term, for example Website PomBase.org (http://ww
cytokinesis (https://www.pombase.org/term/GO:0 w.pombase.org/)
000910) Download URL Downloads (https://ww
View all annotations created from a specific w.pombase.org/dataset
reference, for example 26776736 Chica et al. s)
2016 (https://www.pombase.org/reference/PMID)
Web service URL Genome Browser (http
Genome-wide datasets (including protein datasets, all s://www.pombase.org/jb
annotations, manually curated ortholog lists etc) can be rowse/)
accessed from the datasets (https://www.pombase.org/data Miscellaneous
sets) page. Datasets suitable for display in a genome
browser and that have been loaded can be accessed via the License Public domain
PomBase JBrowse instance (https://www.pombase.org/jbr Curation policy Professionally and
owse/?loc=I%3A1229541..1249541&tracks=PomBase%2 community curated
0forward%20strand%20features%2CPomBase%20revers
Bookmarkable Yes
e%20strand%20features&highlight=).
entities
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[4]

Gene Characterization Status

The GO slim page (https://www.pombase.org/browse-curation/fissi
on-yeast-go-slim-terms) provides an overview of the "biological An overview of data provided by
role" of all "known" fission yeast genes - these are proteins that PomBase and ways to access it.
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,[5] 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 (https://www.pombase.org/gene_subset/non_go_slim_without_bp_annotation). The priority
unstudied genes (https://www.pombase.org/status/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,[6] has been developed. Community curation is reviewed by PomBase staff, and
this results in highly accurate, effectively co-curated, annotations.[7]

PomBase maintains an annotation stats page (https://curation.pombase.org/pombe/stats/annotation).

Knowledgebase Updates
News updates on the PomBase homepage (https://www.pombase.org/)
Posts to the research community mailing list (https://lists.cam.ac.uk/mailman/listinfo/ucam-po
mbelist)
NAR ([Nucleic Acids Research]) database updates
Tweets (@PomBase (https://twitter.com/pombase?lang=en))
Facebook group (https://www.facebook.com/pombase/?jazoest=2651001211166574981031
031169074119109109105119805011180874950901211091195683908872761107112074
105761196510556521195865100120707755111971081211228511367116879985102481
0370684512210256825212210910983118111111568911366104119874987103)
Linkedin group (https://www.linkedin.com/groups/5122686/)

Documentation
Pombase provides both documentation (https://www.pombase.org/documentation) and an FAQ (https://ww
w.pombase.org/faq).

Usage of PomBase as a research tool is explored in the "Eukaryotic Genomic Databases" (Methods and
Protocols) book chapter.[8] Developments and updates are described in the NAR Database Issue
papers.[9][10][1]

For a detailed overview of using S. pombe as a model organism see the genetics primer [11]

References
1. 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" (https://www.ncbi.nlm.nih.g
ov/pmc/articles/PMC6324063). Nucleic Acids Research. 47 (D1): D821–D827.
doi:10.1093/nar/gky961 (https://doi.org/10.1093%2Fnar%2Fgky961). PMC 6324063 (https://
www.ncbi.nlm.nih.gov/pmc/articles/PMC6324063). PMID 30321395 (https://pubmed.ncbi.nl
m.nih.gov/30321395).
2. Wood, V; Carbon, S; Harris, MA; Lock, A; Engel, SR; Hill, DP; Van Auken, K; Attrill, H;
Feuermann, M; Gaudet, P; Lovering, RC; Poux, S; Rutherford, KM; Mungall, CJ (September
2020). "Term Matrix: a novel Gene Ontology annotation quality control system based on
ontology term co-annotation patterns" (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC75360
87). Open Biology. 10 (9): 200149. doi:10.1098/rsob.200149 (https://doi.org/10.1098%2Frso
b.200149). PMC 7536087 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7536087).
PMID 32875947 (https://pubmed.ncbi.nlm.nih.gov/32875947).
3. Harris MA, Lock A, Bähler J, Oliver SG, Wood V (July 2013). "FYPO: The Fission Yeast
Phenotype Ontology" (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3694669).
Bioinformatics. 29 (13): 1671–8. doi:10.1093/bioinformatics/btt266 (https://doi.org/10.1093%
2Fbioinformatics%2Fbtt266). PMC 3694669 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC
3694669). PMID 23658422 (https://pubmed.ncbi.nlm.nih.gov/23658422).
4. Montecchi-Palazzi, L; Beavis, R; Binz, PA; Chalkley, RJ; Cottrell, J; Creasy, D; Shofstahl, J;
Seymour, SL; Garavelli, JS (August 2008). "The PSI-MOD community standard for
representation of protein modification data". Nature Biotechnology. 26 (8): 864–6.
doi:10.1038/nbt0808-864 (https://doi.org/10.1038%2Fnbt0808-864). PMID 18688235 (https://
pubmed.ncbi.nlm.nih.gov/18688235). S2CID 205270043 (https://api.semanticscholar.org/Co
rpusID:205270043).
5. 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?" (https://w
ww.ncbi.nlm.nih.gov/pmc/articles/PMC6395881). Open Biology. 9 (2): 180241.
doi:10.1098/rsob.180241 (https://doi.org/10.1098%2Frsob.180241). PMC 6395881 (https://w
ww.ncbi.nlm.nih.gov/pmc/articles/PMC6395881). PMID 30938578 (https://pubmed.ncbi.nlm.
nih.gov/30938578).
6. Rutherford KM, Harris MA, Lock A, Oliver SG, Wood V (June 2014). "Canto: an online tool
for community literature curation" (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4058955).
Bioinformatics. 30 (12): 1791–2. doi:10.1093/bioinformatics/btu103 (https://doi.org/10.1093%
2Fbioinformatics%2Fbtu103). PMC 4058955 (https://www.ncbi.nlm.nih.gov/pmc/articles/PM
C4058955). PMID 24574118 (https://pubmed.ncbi.nlm.nih.gov/24574118).
7. Lock, A; Harris, MA; Rutherford, K; Hayles, J; Wood, V (1 January 2020). "Community
curation in PomBase: enabling fission yeast experts to provide detailed, standardized,
sharable annotation from research publications" (https://www.ncbi.nlm.nih.gov/pmc/articles/
PMC7192550). Database: The Journal of Biological Databases and Curation. 2020.
doi:10.1093/database/baaa028 (https://doi.org/10.1093%2Fdatabase%2Fbaaa028).
PMC 7192550 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7192550). PMID 32353878
(https://pubmed.ncbi.nlm.nih.gov/32353878).
8. Lock, A; Rutherford, K; Harris, MA; Wood, V (2018). PomBase: The Scientific Resource for
Fission Yeast. Methods in Molecular Biology. Vol. 1757. pp. 49–68. doi:10.1007/978-1-4939-
7737-6_4 (https://doi.org/10.1007%2F978-1-4939-7737-6_4). ISBN 978-1-4939-7736-9.
PMC 6440643 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6440643). PMID 29761456
(https://pubmed.ncbi.nlm.nih.gov/29761456).
9. Wood V, Harris MA, McDowall MD, Rutherford K, Vaughan BW, Staines DM, Aslett M, Lock
A, Bähler J, Kersey PJ, Oliver SG (January 2012). "PomBase: a comprehensive online
resource for fission yeast" (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3245111). Nucleic
Acids Res. 40 (Database issue): D695–9. doi:10.1093/nar/gkr853 (https://doi.org/10.1093%2
Fnar%2Fgkr853). PMC 3245111 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3245111).
PMID 22039153 (https://pubmed.ncbi.nlm.nih.gov/22039153).
10. McDowall MD, Harris MA, Lock A, Rutherford K, Staines DM, Bähler J, Kersey PJ, Oliver
SG, Wood V (January 2015). "PomBase 2015: updates to the fission yeast database" (http
s://www.ncbi.nlm.nih.gov/pmc/articles/PMC4383888). Nucleic Acids Res. 43 (Database
issue): D656–61. doi:10.1093/nar/gku1040 (https://doi.org/10.1093%2Fnar%2Fgku1040).
PMC 4383888 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4383888). PMID 25361970
(https://pubmed.ncbi.nlm.nih.gov/25361970).
11. Hoffman CS, Wood V, Fantes PA (October 2015). "An Ancient Yeast for Young Geneticists: A
Primer on the Schizosaccharomyces pombe Model System" (https://www.ncbi.nlm.nih.gov/p
mc/articles/PMC4596657). Genetics. 201 (2): 403–23. doi:10.1534/genetics.115.181503 (htt
ps://doi.org/10.1534%2Fgenetics.115.181503). PMC 4596657 (https://www.ncbi.nlm.nih.go
v/pmc/articles/PMC4596657). PMID 26447128 (https://pubmed.ncbi.nlm.nih.gov/26447128).

External links
PomBase (http://www.pombase.org)

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