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Val Wood

The PomBase group develops and maintains the 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. 

Current Projects

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. PomBase website code (developed by Kim Rutherford in the PomBase team), is generic and can be easily be configured for other species.

Fission Yeast Community Curation Initiative  To manage the increase in published functional data, PomBase has established a successful community curation project in which authors can easily, without specific training, contribute detailed and structured annotation from their own research publications for 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, Kim Rutherford in the PomBase team has 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 multigene 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. Canto is now used by PHI-base for the curation of pathogen-host interaction phenotype/genotype associations (meta-genotypes), and by FlyBase for phenotype curation.

Representing Phenotype Data 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, using 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. During our current funding cycle, we will use these curated networks to seed the automated biological pathway visualization based on curated data.

"Unknowns" protein inventories  Proteins widely conserved in eukaryotic lineages play fundamentally important roles in the shared, basic mechanisms of life.  The success of many scientific pursuits in biology from basic science to drug discovery depend increasingly on the comprehensive representation of an organism's biology. A complete understanding of protein components conserved throughout eukaryotes would have far-reaching benefits for biological research 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. We recently published preliminary inventories proteins of "unknown biological role" in yeast (fission and budding) and human using a scalable and maintainable method based on GO process slims.

Annotation QC procedures
As part of our commitment to curation accuracy, we develop quality control methods to identify annotation errors and omissions, and to ensure annotation good practice both within PomBase, and to advocate their implementation across other databases. For example, the "Term Matrix" project uses the observation that some GO biological processes are rarely connected to each other (because they functionally, temporally or spatially distant) to identify pairs of biological processes which were unlikely to be co-annotated to the same gene products (e.g. amino acid metabolism and cytokinesis). Annotations are inspected, and either validated or corrected and rules are created to alert curators and ontology editors of potential errors. 

Enquiries

For more information about any of our projects please e-mail the PomBase helpdesk (helpdesk@pombase.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

Valerie Wood, Curation and Project Manager

 

Collaborators

Bähler laboratory (University College London, London, UK)

Monarch Initiative

Gene Ontology Consortium (GO council member)

PHI-base (Rothamsted Research Institute)

Nurse and Hayles Cell Cycle Laboratory (CRUK, London, UK)

BioGRID (Montreal, Canada)

 FlyBase (University of Cambridge, UK)

Selected Publications

Community curation in PomBase: enabling fission yeast experts to provide detailed, standardized, sharable annotation from research publications.
Lock A, Harris MA, Rutherford K, Hayles J, Wood V. Database (Oxford). 2020 Jan 1;2020:baaa028.

PHI-base: the pathogen-host interactions database.
Urban M, Cuzick A, Seager J, Wood V, Rutherford K, Venkatesh SY, De Silva N, Martinez MC, Pedro H, Yates AD, Hassani-Pak K, Hammond-Kosack KE. Nucleic Acids Res. 2020 Jan 8;48(D1):D613-D620.

Hidden in plain sight: what remains to be discovered in the eukaryotic proteome?
Wood V, Lock A, Harris MA, Rutherford K, Bähler J, Oliver SG. Open Biol. 2019 Feb 28;9(2):180241.

PomBase 2018: user-driven reimplementation of the fission yeast database provides rapid and intuitive access to diverse, interconnected information.
Lock A, Rutherford K, Harris MA, Hayles J, Oliver SG, Bähler J; Wood V. Nucleic Acids Res. 2018 (Database issue)

Model organism databases: essential resources that need the support of both funders and users.
Oliver SG, Lock A, Harris MA, Nurse P, Wood V. BMC Biol. 2016 14(1): 49.

PomBase 2015: updates to the fission yeast database.
McDowall MD, Harris MA, Lock A, Rutherford K, Staines DM, Bähler J, Kersey PJ, Oliver SG, Wood V. Nucleic Acids Res. 2014 Oct 31. 

A method for increasing expressivity of Gene Ontology annotations using a compositional approach. BMC Bioinformatics. 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.  2014 May 21;15(1):155.

Canto: An online tool for community literature curation. Bioinformatics.
Rutherford KM, Harris MA, Lock A, Oliver SG, Wood V. 2014.

Improving functional annotation for industrial microbes: a case study with Pichia pastoris.
Dikicioglu D, Wood V, Rutherford KM, McDowall MD, Oliver SG. Trends Biotechnol. 2014 Aug;32(8):396-9.

A genome-wide resource of cell cycle and cell shape genes of fission yeast.
Hayles J, Wood V, Jeffery L, Hoe K-L, Kim D-U, Park H-O, Salas-Pino S, Heichinger C, Nurse P. Open Biol 2013 3: 130053.

FYPO: The Fission Yeast Phenotype Ontology.
Harris MA, Lock A, Bähler J, Oliver SG, Wood V. Bioinformatics. 2013.

Gene Ontology annotations and resources.
The Gene Ontology Consortium. Nucleic Acids Res. 2013 Jan;41(Database issue):

On the use of gene ontology annotations to assess functional similarity among orthologs and paralogs: A short report
Thomas PD, Wood V, Mungall CJ, Lewis SE, Blake JA. PLoS Comput Biol. 2012 8(2)

PomBase: A comprehensive online resource for fission yeast.
Wood V, Harris MA, McDowall MD, Rutherford K, Vaughan BW, Staines DM, Aslett M, Lock A, Bähler J, Kersey, Oliver SG. Nucleic Acids Res. 2012 Jan;40(D1): D559-D564

The Gene Ontology: Enhancements for 2011.
Gene Ontology Consortium. Nucleic Acids Res. 2012 Jan;40(D1):D D559-D564

Augmented annotation of the Schizosaccharomyces pombe genome reveals additional genes required for growth and viability.
Bitton D, Wood V, Scutt PJ, Grallert A, Yates T, Smith DL, Hagan IM, Miller CJ. Genetics 2011 187, 4

Analysis of a genome-wide set of gene deletions in the fission yeast Schizosaccharomyces pombe.
Kim DU, Hayles J, Kim D, Wood V, et al. Nature Biotechnology 2010 28, 617–623

The Gene Ontology's Reference Genome Project: A Unified Framework for Functional Annotation across Species.
The Reference Genome Group of the Gene Ontology Consortium. PLoS Computational Biol. 2009 5(7)

AmiGO Hub; Web Presence Working Group; AmiGO: Online access to ontology and annotation data.
Carbon S, Ireland A, Mungall CJ, Shu S, Marshall B, Lewis S. Bioinformatics. 2009 15;25(2):288-9.

Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution.
Wilhelm BT, Marguerat S, Watt S, Schubert F, Wood V, Goodhead I, Penkett CJ, Rogers J, Bähler J. Nature. 2008 Jun 26;453(7199):1239-43

Use and misuse of Gene Ontology annotations.
Rhee SY, Wood V, Dolinski K, Draghici S. Nat Rev Genet. 2008 Jul;9(7):509-15.

The Gene Ontology (GO) project in 2008.
Gene Ontology Consortium. 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

Schizosaccharomyces pombe comparative genomics; from sequence to systems.
Wood V. In: Comparative Genomics using fungi as models (P. Sunnerhagen, J. Piskur, eds.) Topics in Current Genetics vol 15, pp 233- 285 (2006)

Gene Ontology annotation status of the fission yeast genome: preliminary coverage approaches 100%.
Aslett M and Wood V. Yeast. 2006 Oct 15;23(13)913-919)

YOGY: a web-based, integrated database to retrieve protein orthologs and associated Gene Ontology terms.
Penkett CJ, Morris JA, Wood V, Bahler J. Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W330-4.

The Gene Ontology (GO) project in 2006.
Gene Ontology Consortium. Nucleic Acids Res. 2006 Jan 1;34(Database issue):D322-6.

The Gene Ontology (GO) database and informatics resource.
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. Nucleic Acids Res. 2004 Jan 1;32(Database issue):D258-61.

Retrotransposons and their recognition of pol II promoters: a comprehensive survey of the transposable elements from the complete genome sequence of Schizosaccharomyces pombe.
Bowen NJ, Jordan IK, Epstein JA, Wood V, Levin HL. Genome Res. 2003 Sep;13(9):1984-97

The genome sequence of Schizosaccharomyces pombe.
Wood V, Gwilliam R, Rajandream, M-A, Lyne M et al. Nature. 2002 Feb 21;415(6874):871-80.

A reannotation of the Saccharomyces cerevisiae genome.
Wood V, Rutherford K, Ivens A, Rajandream M-A, Barrell BG. Comparative and Functional Genomics 2001 2:143-154