The PomBase group develops and maintains a curated Model Organism Database for the fission yeast (Schizosaccharomyces pombe). Fission yeast is a well-studied single-celled fungus (yeast) used intensively as a model to study many conserved cellular processes including the cell cycle and chromosome segregation, that are frequently implicated in heritable human diseases and cancers.
PomBase A comprehensive online database for the fission yeast Schizosaccharomyces pombe, providing genome feature and functional annotation, literature curation and access to large-scale data sets.
Fission Yeast Community Curation Initiative To deal with the increase in published functional data, PomBase has established a novel community curation initiative in which authors can easily, without specific training, contribute detailed and structured annotation from their own research publications for approval by dedicated curators, inclusion in PomBase and dissemination to other databases.
Canto Curation Tool Detailed curation of published molecular and genetic data is essential for any model organism database. To support curation by both professional curators and the fission yeast community we have developed Canto, an intuitive web-based interface to support literature curation using ontologies, and a literature management environment. Within PomBase, Canto currently supports annotation of GO terms, phenotype data (single and multi gene phenotypes), protein modifications, genetic and physical interactions. Canto is a generic component of the GMOD project and can be easily configured for use with other organisms, and ontologies.
Phenotype Data Representation The identification of novel phenotypes drives much biological research from the uncovering of disease phenotypes to the manipulation of model systems like yeast. However, the cross-species integration of phenotype annotation is currently hindered by the absence of an equivalent infrastructure to that provided by the GO consortium for functional data. To aid future interoperability of phenotype curation we provide detailed cellular phenotype annotation supported by the development of FYPO, a formally defined ontology of pre-composed cellular phenotypes. Critically, PomBase phenotype annotation also supplies two additional requirements for accurate data interpretation and exploitation: 1. Annotations are linked to a description of the underlying genomic lesion. Our system also allows annotation of phenotypes at the level of the genotype where alleles of multiple genes contribute to an observed phenotype. 2. Experimental conditions under which the phenotype was observed are captured.
Curated High Confidence Physical Interaction Networks As part of the PomBase project, in collaboration with esyN we have piloted a system to generate high quality physical networks directly from Gene Ontology annotation data. We are currently using these networks to target literature curation gaps.
Identification of conserved "Unknowns" Proteins conserved widely among eukaryotes play fundamentally important roles in the shared, basic mechanisms of life. The success of many endeavours in basic and translational research, including drug discovery, metabolomics, and systems biology, depends critically on comprehensive representation of conserved functions. A more complete understanding of protein components conserved throughout eukaryotes would have far-reaching benefits for biological research in many species and on a wide range of scales. However, despite almost a century of gene- and gene product-specific genetic and biochemical investigation the roles of many broadly conserved proteins remain unknown. PomBase provides an inventory of "Priority unstudied genes" conserved from fission yeast to vertebrates.
GO annotation QC annotation protocols
As part of our commitment to curation accuracy, breadth and specificity we are developing quality control methods to identify annotation errors and omissions, and SOPs to ensure annotation good practice within PomBase, and to advocate their implementation across other databases. For example, some biological processes are rarely connected to each other because they functionally, temporally or spatially distant. We therefore speculated that we could identify pairs of biological processes which were unlikely to be co-annotated to the same gene products (e.g. amino acid metabolism and cytokinesis), and use these to create curation rules. These rules have been used to alert curators and ontology editors of potential errors and resulted in the correction of large numbers of annotation and ontology errors. Another mechanism to improve annotation is the identification of GO terms (currently 1119 terms for fission yeast) where a more specific annotation should always be possible.
For more information about any of our projects please e-mail the PomBase helpdesk (firstname.lastname@example.org). For general enquiries about fission yeast (tools, methods, conferences, courses, workshops etc) we maintain a community mailing list 'pombelist'.
PomBase Group Members
Midori Harris, Curation and project lead for phenotype ontology development
Kim Rutherford (Cambridge University and University of Otago, New Zealand), project lead for Chado curation database and curation tool development
Antonia Lock (UCL), Curation and condition ontology development
Mark McDowall (EBI), PomBase website development, Ensembl Genomes
Valerie Wood, Curation and Project Manager
Bähler laboratory (University College London, London, UK)
Ensembl Genomes (EBI, Hinxton, UK)
Gene Ontology Consortium (member)
Chris Brown (University of Otago, New Zealand)
Nurse and Hayles Cell Cycle Laboratory (CRUK, London, UK)
BioGRID (Montreal, Canada)
McDowall MD, Harris MA, Lock A, Rutherford K, Staines DM, Bähler J, Kersey PJ, Oliver SG, Wood V. PomBase 2015: updates to the fission yeast database. Nucleic Acids Res. 2014 Oct 31.
Huntley RP, Harris MA, Alam-Faruque Y, Blake JA, Carbon S, Dietze H, Dimmer EC, Foulger RE, Hill DP, Khodiyar VK, Lock A, Lomax J, Lovering RC, Mutowo-Meullenet P, Sawford T, Van Auken K, Wood V, Mungall CJ. A method for increasing expressivity of Gene Ontology annotations using a compositional approach. BMC Bioinformatics. 2014 May 21;15(1):155.
Rutherford KM, Harris MA, Lock A, Oliver SG, Wood V. Canto: An online tool for community literature curation. Bioinformatics. 2014 Epub ahead of print.
Dikicioglu D, Wood V, Rutherford KM, McDowall MD, Oliver SG. Improving functional annotation for industrial microbes: a case study with Pichi pastoris. Trends Biotechnol. 2014 Aug;32(8):396-9.
Hayles J, Wood V, Jeffery L, Hoe K-L, Kim D-U, Park H-O, Salas-Pino S, Heichinger C, Nurse P. A genome-wide resource of cell cycle and cell shape genes of fission yeast. Open Biol 2013 3: 130053.
Harris MA, Lock A, Bähler J, Oliver SG, Wood V. FYPO: The Fission Yeast Phenotype Ontology.
The Gene Ontology Consortium/ Gene Ontology annotations and resources. Nucleic Acids Res. 2013 Jan;41(Database issue):
Thomas PD, Wood V, Mungall CJ, Lewis SE, Blake JA. On the use of gene ontology annotations to assess functional similarity among orthologs and paralogs: A short report.PLoS Comput Biol. 2012 8(2)
Wood V, Harris MA, McDowall MD, Rutherford K, Vaughan BW, Staines DM, Aslett M, Lock A, Bahler J, Kersey, Oliver SG. PomBase: A comprehensive online resource for fission yeast. Nucleic Acids Res. 2012 Jan;40(D1): D559-D564
Gene Ontology Consortium. The Gene Ontology: Enhancements for 2011. Nucleic Acids Res. 2012 Jan;40(D1):D D559-D564
Bitton D, Wood V, Scutt PJ, Grallert A, Yates T, Smith DL, Hagan IM, Miller CJ. Augmented annotation of the Schizosaccharomyces pombe genome reveals additional genes required for growth and viability. Genetics 2011 187, 4
Kim DU, Hayles J, Kim D, Wood V, et. al. Analysis of a genome-wide set of gene deletions in the fission yeast Schizosaccharomyces pombe Nature Biotechnology 2010 28, 617–623
The Reference Genome Group of the Gene Ontology Consortium. The Gene Ontology's Reference Genome Project: A Unified Framework for Functional Annotation across Species. PLoS Computational Biol. 2009 5(7)
Carbon S, Ireland A, Mungall CJ, Shu S, Marshall B, Lewis S, AmiGO Hub; Web Presence Working Group; AmiGO: Online access to ontology and annotation data.Bioinformatics. 2009 15;25(2):288-9.
Wilhelm BT, Marguerat S, Watt S, Schubert F, Wood V, Goodhead I, Penkett CJ, Rogers J, Bähler J; Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution. Nature 2008 Jun 26;453(7199):1239-43
Rhee SY, Wood V, Dolinski K, Draghici S; Use and misuse of Gene Ontology annotations. Nat Rev Genet. 2008 Jul;9(7):509-15.
Gene Ontology Consortium; The Gene Ontology (GO) project in 2008.Nucleic Acids Res. 2008 Jan;36(Database issue):D440-4
The BioGRID Interaction Database: 2008 update. Breitkreutz BJ, Stark C, Reguly T, Boucher L, Breitkreutz A, Livstone M, Oughtred R, Lackner DH, Bähler J, Wood V, Dolinski K, Tyers M Nucleic Acids Res. 2008 January; 36(Database issue): D637–D640
Wood V; Schizosaccharomyces pombe comparative genomics; from sequence to systems. In: Comparative Genomics using fungi as models (P. Sunnerhagen, J. Piskur, eds.) Topics in Current Genetics vol 15, pp 233- 285 (2006)
Aslett M and Wood V; Gene Ontology annotation status of the fission yeast genome: preliminary coverage approaches 100%. Yeast. 2006 Oct 15;23(13)913-919)
Penkett CJ, Morris JA, Wood V, Bahler J; YOGY: a web-based, integrated database to retrieve protein orthologs and associated Gene Ontology terms. Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W330-4.
Gene Ontology Consortiom; The Gene Ontology (GO) project in 2006.Nucleic Acids Res. 2006 Jan 1;34(Database issue):D322-6.
Harris MA, Clark J, Ireland A, Lomax J, Ashburner M, Foulger R, Eilbeck K, Lewis S, Marshall B, Mungall C, Richter J, Rubin GM, Blake JA, Bult C, Dolan M, Drabkin H, Eppig JT, Hill DP, Ni L, Ringwald M, Balakrishnan R, Cherry JM, Christie KR, Costanzo MC, Dwight SS, Engel S, Fisk DG, Hirschman JE, Hong EL, Nash RS, Sethuraman A, Theesfeld CL, Botstein D, Dolinski K, Feierbach B, Berardini T, Mundodi S, Rhee SY, Apweiler R, Barrell D, Camon E, Dimmer E, Lee V, Chisholm R, Gaudet P, Kibbe W, Kishore R, Schwarz EM, Sternberg P, Gwinn M, Hannick L, Wortman J, Berriman M, Wood V, de la Cruz N, Tonellato P, Jaiswal P, Seigfried T, White R. The Gene Ontology (GO) database and informatics resource. Nucleic Acids Res. 2004 Jan 1;32(Database issue):D258-61.
Bowen NJ, Jordan IK, Epstein JA, Wood V, Levin HL. Retrotransposons and their recognition of pol II promoters: a comprehensive survey of the transposable elements from the complete genome sequence of Schizosaccharomyces pombe. Genome Res. 2003 Sep;13(9):1984-97
V Wood Gwilliam R, Rajandream, M-A, Lyne M et al The genome sequence of Schizosaccharomyces pombe. Nature. 2002 Feb 21;415(6874):871-80.
V Wood, Rutherford K, Ivens A, Rajandream M-A, Barrell BG. A reannotation of the Saccharomyces cerevisiae genome Comparative and Functional Genomics 2001 2:143-154