Damian Smedley

Summary

Affiliation: Wellcome Trust Genome Campus
Country: UK

Publications

  1. pmc XGAP: a uniform and extensible data model and software platform for genotype and phenotype experiments
    Morris A Swertz
    Genomics Coordination Center, Department of Genetics, University Medical Center Groningen and University of Groningen, Groningen, The Netherlands
    Genome Biol 11:R27. 2010
  2. pmc Towards the integration of mouse databases - definition and implementation of solutions to two use-cases in mouse functional genomics
    Michael Gruenberger
    Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3EG, UK
    BMC Res Notes 3:16. 2010
  3. pmc Finding and sharing: new approaches to registries of databases and services for the biomedical sciences
    Damian Smedley
    European Bioinformatics Institute, Genome Campus, Hinxton, Cambridgeshire, CB10 1SA
    Database (Oxford) 2010:baq014. 2010
  4. pmc BioMart--biological queries made easy
    Damian Smedley
    Ontario Institute for Cancer Research, MaRS Centre, 101 College Street, Toronto, Ontario, Canada
    BMC Genomics 10:22. 2009
  5. doi request reprint Solutions for data integration in functional genomics: a critical assessment and case study
    Damian Smedley
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
    Brief Bioinform 9:532-44. 2008
  6. pmc Ensembl's 10th year
    Paul Flicek
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Nucleic Acids Res 38:D557-62. 2010
  7. pmc BioMart Central Portal--unified access to biological data
    Syed Haider
    EMBL European Bioinformatics Institute, Hinxton, Cambridge CB10 1SD, Computer Laboratory, University of Cambridge, 15 JJ Thomson Avenue, Cambridge CB3 0FD, UK
    Nucleic Acids Res 37:W23-7. 2009
  8. pmc EnsMart: a generic system for fast and flexible access to biological data
    Arek Kasprzyk
    European Bioinformatics Institute EBI, Hinxton, Cambridge CB10 1SH, UK
    Genome Res 14:160-9. 2004
  9. pmc PhenoDigm: analyzing curated annotations to associate animal models with human diseases
    Damian Smedley
    Mouse Informatics Group, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
    Database (Oxford) 2013:bat025. 2013
  10. pmc EMMA--mouse mutant resources for the international scientific community
    Phil Wilkinson
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Nucleic Acids Res 38:D570-6. 2010

Detail Information

Publications20

  1. pmc XGAP: a uniform and extensible data model and software platform for genotype and phenotype experiments
    Morris A Swertz
    Genomics Coordination Center, Department of Genetics, University Medical Center Groningen and University of Groningen, Groningen, The Netherlands
    Genome Biol 11:R27. 2010
    ..Current functionality includes tools ranging from eQTL analysis in mouse to genome-wide association studies in humans...
  2. pmc Towards the integration of mouse databases - definition and implementation of solutions to two use-cases in mouse functional genomics
    Michael Gruenberger
    Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3EG, UK
    BMC Res Notes 3:16. 2010
    ..abstract:..
  3. pmc Finding and sharing: new approaches to registries of databases and services for the biomedical sciences
    Damian Smedley
    European Bioinformatics Institute, Genome Campus, Hinxton, Cambridgeshire, CB10 1SA
    Database (Oxford) 2010:baq014. 2010
    ..We expect such approaches will result in improved discovery, uptake and utilization of data resources. Database URL: http://www.casimir.org.uk/casimir_ddf...
  4. pmc BioMart--biological queries made easy
    Damian Smedley
    Ontario Institute for Cancer Research, MaRS Centre, 101 College Street, Toronto, Ontario, Canada
    BMC Genomics 10:22. 2009
    ..This is not an efficient solution in terms of cost and time. Instead, it would be better if the biologist only had to learn one generic interface. BioMart provides such a solution...
  5. doi request reprint Solutions for data integration in functional genomics: a critical assessment and case study
    Damian Smedley
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
    Brief Bioinform 9:532-44. 2008
    ..Finally, we focus on the current impediments to adopting such an approach in a wider context, and strategies to overcome them...
  6. pmc Ensembl's 10th year
    Paul Flicek
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Nucleic Acids Res 38:D557-62. 2010
    ....
  7. pmc BioMart Central Portal--unified access to biological data
    Syed Haider
    EMBL European Bioinformatics Institute, Hinxton, Cambridge CB10 1SD, Computer Laboratory, University of Cambridge, 15 JJ Thomson Avenue, Cambridge CB3 0FD, UK
    Nucleic Acids Res 37:W23-7. 2009
    ..The website is free and open to all users and there is no login requirement...
  8. pmc EnsMart: a generic system for fast and flexible access to biological data
    Arek Kasprzyk
    European Bioinformatics Institute EBI, Hinxton, Cambridge CB10 1SH, UK
    Genome Res 14:160-9. 2004
    ..Both implementations and the database are freely available for local installation, and can be extended or adapted to 'non-Ensembl' data sets...
  9. pmc PhenoDigm: analyzing curated annotations to associate animal models with human diseases
    Damian Smedley
    Mouse Informatics Group, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
    Database (Oxford) 2013:bat025. 2013
    ..Furthermore, we provide guidance on how to browse the data with PhenoDigm's web interface and illustrate its usefulness in supporting research. Database URL: http://www.sanger.ac.uk/resources/databases/phenodigm..
  10. pmc EMMA--mouse mutant resources for the international scientific community
    Phil Wilkinson
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Nucleic Acids Res 38:D570-6. 2010
    ..g. Ensembl. Other resources are able to display EMMA data by accessing our Distributed Annotation System server. EMMA database access is publicly available at http://www.emmanet.org...
  11. pmc Ensembl variation resources
    Yuan Chen
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    BMC Genomics 11:293. 2010
    ..Maximising the utility of the data requires that it be stored in an accessible manner that facilitates the integration of variation data with other genome resources such as gene annotation and comparative genomics...
  12. pmc BioMart Central Portal: an open database network for the biological community
    Jonathan M Guberman
    Ontario Institute for Cancer Research, Toronto, M5G 0A3, Canada
    Database (Oxford) 2011:bar041. 2011
    ..Here, we describe the structure of Central Portal and show example queries to demonstrate its capabilities...
  13. pmc TRACER: a resource to study the regulatory architecture of the mouse genome
    Chao Kung Chen
    European Bioinformatics Institute European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    BMC Genomics 14:215. 2013
    ..The mechanisms that control the integration of these diverse inputs into specific gene expression patterns are still poorly understood. New approaches enabling the dissection of these mechanisms in vivo are needed...
  14. pmc BioMart as an integration solution for the International Knockout Mouse Consortium
    Darren J Oakley
    The Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1HH
    Database (Oxford) 2011:bar028. 2011
    ..Here, we describe these datasets in more detail and illustrate the functionality of the portal using several examples...
  15. doi request reprint The International Mouse Phenotyping Consortium Web Portal, a unified point of access for knockout mice and related phenotyping data
    Gautier Koscielny
    European Molecular Biology Laboratory, European Bioinformatics Institute EMBL EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK, Medical Research Council Harwell Mammalian Genetics Unit and Mary Lyon Centre, Harwell, Oxfordshire OX11 0RD, UK and Mouse Informatics Group, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
    Nucleic Acids Res 42:D802-9. 2014
    ..As phenotype data become available for every gene in the mouse, the IMPC web portal will become an invaluable tool for researchers studying the genetic contributions of genes to human diseases. ..
  16. doi request reprint The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data
    Sebastian Kohler
    Institute for Medical Genetics and Human Genetics, Charite Universitatsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany, Berlin Brandenburg Center for Regenerative Therapies, Charite Universitatsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany, Lawrence Berkeley National Laboratory, Mail Stop 84R0171, Berkeley, CA 94720, USA, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK, Department of Medical Genetics, Cambridge University Addenbrooke s Hospital, Cambridge CB2 2QQ, UK, Universite Paul Sabatier, Faculte de Chirurgie Dentaire, CHU Toulouse, France, Centre for Genomic Medicine, Central Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Sciences Centre MAHSC, Manchester, UK, Centre for Genomic Medicine, Institute of Human Development, Faculty of Medical and Human Sciences, University of Manchester, MAHSC, Manchester M13 9WL, UK, Institute of Genetic Medicine Newcastle University, Central Parkway, Newcastle upon Tyne, NE1 3BZ, UK, Department of Computer Science, University of Toronto, Ontario, Canada
    Nucleic Acids Res 42:D966-74. 2014
    ..We have created various ways to access the HPO database content using flat files, a MySQL database, and Web-based tools. All data and documentation on the HPO project can be found online. ..
  17. pmc MouseFinder: Candidate disease genes from mouse phenotype data
    Chao Kung Chen
    Vertebrate Genomics Team, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
    Hum Mutat 33:858-66. 2012
    ..We demonstrate its use in identifying ARTN as a strong candidate gene within the 1p34.1-p32 mapped locus for a hereditary form of ptosis...
  18. doi request reprint Cre recombinase resources for conditional mouse mutagenesis
    Damian Smedley
    European Bioinformatics Institute, Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
    Methods 53:411-6. 2011
    ..The continuously changing landscape of these mouse resources reflects the rapid progression of research and development in conditional and inducible mouse mutagenesis...
  19. doi request reprint Post-publication sharing of data and tools
    Paul N Schofield
    Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, CB2 3EG, UK
    Nature 461:171-3. 2009
    ..Despite existing guidelines on access to data and bioresources, good practice is not widespread. A meeting of mouse researchers in Rome proposes ways to promote a culture of sharing...
  20. pmc An overview of Ensembl
    Ewan Birney
    EMBL European Bioinformatics Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
    Genome Res 14:925-8. 2004
    ....