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Val Wood

PomBase

Our group develops and maintains a curated Model Organism Database (MOD) for the fission yeast (Schizosaccharomyces pombe). Fission yeast  is a well-studied single-celled fungus (yeast) that is used as a model to study many conserved cellular processes that are frequently implicated in heritable human diseases and cancers.  A large and active research community routinely applies molecular genetic, cell biological, and biochemical techniques (>10000 publications). Increasingly, high-throughput approaches are being applied, generating a concomitant increase in data volume.

We aim to provide: i). Comprehensive and deep curation of the scientific literature, partially supported by an extensive community curation initiative ii). Software infrastructure to support curation activities iii). Computational infrastructure to integrate and display the curated data, high-throughput data, and data from other fungal genomes in the context of the Ensembl Genomes project.

The protocols, workflows and software developed by PomBase to support literature curation activities are generic and can be implemented by other organism communities to work with the Chado database schema and Ensembl Genomes to construct organism-specific databases.

For enquiries about 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' (>1000 researchers) (archived posts) .

 

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

 

Current Projects

PomBase A comprehensive database for the fission yeast Schizosaccharomyces pombe, providing structural and functional annotation, literature curation and access to large-scale data sets.

Fission Yeast Phenotype Ontology (FYPO) a formal ontology of phenotypes observed in fission yeast developed to support the comprehensive and detailed representation of phenotypes in PomBase.

CANTO  is a GMOD-compliant web based literature management and curation tool developed for the fission yeast community and professional curators to curate genetic and molecular data for inclusion in PomBase and dissemination to other databases. Canto is a generic tool and can be easily configured for use with other organisms. You can try the demo tool here

The fission yeast community curation initiative was launched  at Pombe 2013 (London 24-29 June 2013) , see PomBase for more  information on this project

 

Collaborators

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)

Ruth Lovering (University College London, London, UK)

BioGRID (Montreal, Canada)

 

Selected Publications

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.

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.
Bioinformatics. 2013 Epub ahead of print.

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