Philip Jones

Summary

Affiliation: Wellcome Trust Genome Campus
Country: UK

Publications

  1. ncbi Dasty and UniProt DAS: a perfect pair for protein feature visualization
    Philip Jones
    EMBL Outstation European Bioinformatics Institute EBI, Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD, UK
    Bioinformatics 21:3198-9. 2005
  2. doi Analysing proteomics identifications in the context of functional and structural protein annotation: integrating annotation using PICR, DAS, and BioMart
    Philip Jones
    European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK
    Methods Mol Biol 696:107-21. 2011
  3. pmc PRIDE: new developments and new datasets
    Philip Jones
    EMBL Outstation, European Bioinformatics Institute EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
    Nucleic Acids Res 36:D878-83. 2008
  4. doi Using the PRIDE proteomics identifications database for knowledge discovery and data analysis
    Philip Jones
    EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Methods Mol Biol 604:297-307. 2010
  5. pmc The InterPro BioMart: federated query and web service access to the InterPro Resource
    Philip Jones
    EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
    Database (Oxford) 2011:bar033. 2011
  6. pmc PRIDE: a public repository of protein and peptide identifications for the proteomics community
    Philip Jones
    EMBL Outstation, European Bioinformatics Institute EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
    Nucleic Acids Res 34:D659-63. 2006
  7. pmc The Protein Identifier Cross-Referencing (PICR) service: reconciling protein identifiers across multiple source databases
    Richard G Côté
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1QY, UK
    BMC Bioinformatics 8:401. 2007
  8. pmc The Ontology Lookup Service: more data and better tools for controlled vocabulary queries
    Richard G Côté
    EMBL Outstation, European Bioinformatics Institute EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
    Nucleic Acids Res 36:W372-6. 2008
  9. ncbi Submit your interaction data the IMEx way: a step by step guide to trouble-free deposition
    Sandra Orchard
    European Bioinformatics Institute, Hinxton, Cambridge, UK
    Proteomics 7:28-34. 2007
  10. pmc Integrating biological data--the Distributed Annotation System
    Andrew M Jenkinson
    European Bioinformatics Institute, Hinxton, Cambridge, CB10 1SD, UK
    BMC Bioinformatics 9:S3. 2008

Detail Information

Publications22

  1. ncbi Dasty and UniProt DAS: a perfect pair for protein feature visualization
    Philip Jones
    EMBL Outstation European Bioinformatics Institute EBI, Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD, UK
    Bioinformatics 21:3198-9. 2005
    ....
  2. doi Analysing proteomics identifications in the context of functional and structural protein annotation: integrating annotation using PICR, DAS, and BioMart
    Philip Jones
    European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK
    Methods Mol Biol 696:107-21. 2011
    ....
  3. pmc PRIDE: new developments and new datasets
    Philip Jones
    EMBL Outstation, European Bioinformatics Institute EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
    Nucleic Acids Res 36:D878-83. 2008
    ..Collaboration with groups outside the EBI has been fruitful in extending PRIDE, including an approach to encode iTRAQ quantitative data in PRIDE XML...
  4. doi Using the PRIDE proteomics identifications database for knowledge discovery and data analysis
    Philip Jones
    EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Methods Mol Biol 604:297-307. 2010
    ..We also explore how complex queries can be constructed using the PRIDE BioMart. Finally, we will describe how the user can integrate PRIDE data with annotation from other resources, using federated BioMart queries...
  5. pmc The InterPro BioMart: federated query and web service access to the InterPro Resource
    Philip Jones
    EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
    Database (Oxford) 2011:bar033. 2011
    ..Database URL: http://www.ebi.ac.uk/interpro/biomart/martview...
  6. pmc PRIDE: a public repository of protein and peptide identifications for the proteomics community
    Philip Jones
    EMBL Outstation, European Bioinformatics Institute EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
    Nucleic Acids Res 34:D659-63. 2006
    ..Data can be retrieved as machine-readable PRIDE or mzData XML (the latter for mass spectra without identifications), or as human-readable HTML...
  7. pmc The Protein Identifier Cross-Referencing (PICR) service: reconciling protein identifiers across multiple source databases
    Richard G Côté
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1QY, UK
    BMC Bioinformatics 8:401. 2007
    ..As a result, we have not found a solution that is generic enough and broad enough in mapping scope to suit our needs...
  8. pmc The Ontology Lookup Service: more data and better tools for controlled vocabulary queries
    Richard G Côté
    EMBL Outstation, European Bioinformatics Institute EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
    Nucleic Acids Res 36:W372-6. 2008
    ..Improvements have been made to both OLS query interfaces, based on user feedback and requirements, to improve usability and service interoperability and provide novel ways to perform queries...
  9. ncbi Submit your interaction data the IMEx way: a step by step guide to trouble-free deposition
    Sandra Orchard
    European Bioinformatics Institute, Hinxton, Cambridge, UK
    Proteomics 7:28-34. 2007
    ..This article walks the potential submitter through the various routes by which data may be deposited with the databases and describes the tools which have been developed to assist in this process...
  10. pmc Integrating biological data--the Distributed Annotation System
    Andrew M Jenkinson
    European Bioinformatics Institute, Hinxton, Cambridge, CB10 1SD, UK
    BMC Bioinformatics 9:S3. 2008
    ..DAS continues to expand its applicability and evolve in response to new challenges facing integrative bioinformatics...
  11. doi The PRIDE proteomics identifications database: data submission, query, and dataset comparison
    Philip Jones
    EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Methods Mol Biol 484:287-303. 2008
    ..PRIDE can be accessed at http://www.ebi.ac.uk/pride...
  12. doi Analysis of the experimental detection of central nervous system-related genes in human brain and cerebrospinal fluid datasets
    Michael Mueller
    EMBL Outstation, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Proteomics 8:1138-48. 2008
    ..We also evaluate the empirically observed peptides of interest against predictions of their proteotypic character...
  13. pmc EBI metagenomics--a new resource for the analysis and archiving of metagenomic data
    Sarah Hunter
    European Molecular Biology Laboratory, European Bioinformatics Institute EMBL EBI, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, UK, Oxford e Research Centre, University of Oxford, 7 Keble Road, Oxford, OX1 3QG, UK and NERC Centre for Ecology and Hydrology, Maclean Building, Benson Lane, Crowmarsh Gifford, Wallingford, OX10 8BB, UK
    Nucleic Acids Res 42:D600-6. 2014
    ....
  14. pmc The Ontology Lookup Service, a lightweight cross-platform tool for controlled vocabulary queries
    Richard G Côté
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    BMC Bioinformatics 7:97. 2006
    ..We saw the need for a centralized location to perform controlled vocabulary queries that would offer both a lightweight web-accessible user interface as well as a consistent, unified SOAP interface for automated queries...
  15. ncbi Proteomic data exchange and storage: the need for common standards and public repositories
    Sandra Orchard
    EMBL Outstation Hinxton, European Bioinformatics Institute, Cambridge, UK
    Methods Mol Biol 367:261-70. 2007
    ..Accompanying controlled vocabularies allow the accurate, while systematic, representation of metadata throughout both schema...
  16. pmc InterPro in 2011: new developments in the family and domain prediction database
    Sarah Hunter
    EMBL Outstation European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SD Cambridge, UK
    Nucleic Acids Res 40:D306-12. 2012
    ..Herein we give an overview of new developments in the database and its associated software since 2009, including updates to database content, curation processes and Web and programmatic interfaces...
  17. pmc InterProScan 5: genome-scale protein function classification
    Philip Jones
    European Molecular Biology Laboratory, European Bioinformatics Institute EMBL EBI, Wellcome Trust Genome Campus, Hinxton CB10 1SD and Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
    Bioinformatics 30:1236-40. 2014
    ..InterProScan is freely available for download from the EMBl-EBI FTP site and the open source code is hosted at Google Code...
  18. pmc Metagenomic analysis: the challenge of the data bonanza
    Chris I Hunter
    European Bioinformatics Institute, Cambridge, UK
    Brief Bioinform 13:743-6. 2012
    ..Herein, we describe some of the bioinformatic approaches currently used by metagenomics researchers to analyze their data, the issues they face and the steps that could be taken to help overcome these challenges...
  19. ncbi Proteomics and Beyond: a report on the 3rd Annual Spring Workshop of the HUPO-PSI 21-23 April 2006, San Francisco, CA, USA
    Sandra Orchard
    EMBL Outstation European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, UK
    Proteomics 6:4439-43. 2006
    ....
  20. ncbi Automated reprocessing pipeline for searching heterogeneous mass spectrometric data of the HUPO Brain Proteome Project pilot phase
    Christian Stephan
    Medizinisches Proteom Center, Ruhr Universitat Bochum, Bochum, Germany
    Proteomics 6:5015-29. 2006
    ....
  21. ncbi PRIDE: the proteomics identifications database
    Lennart Martens
    Department of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
    Proteomics 5:3537-45. 2005
    ..The complete PRIDE database, source code, data, and support tools are freely available for web access or download and local installation...
  22. pmc ISPIDER Central: an integrated database web-server for proteomics
    Jennifer A Siepen
    Faculty of Life Sciences, University of Manchester, M13 9PT, UK
    Nucleic Acids Res 36:W485-90. 2008
    ..This web server offers the first truly integrated access to proteomics repositories and provides a unique service to biologists interested in mass spectrometry-based proteomics...