Research Topics
| Philip JonesSummaryAffiliation: Wellcome Trust Genome Campus Country: UK Publications
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Detail Information
Publications
Dasty and UniProt DAS: a perfect pair for protein feature visualizationPhilip Jones
EMBL Outstation European Bioinformatics Institute EBI, Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD, UK
Bioinformatics 21:3198-9. 2005....
The InterPro BioMart: federated query and web service access to the InterPro ResourcePhilip 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...- PRIDE: a public repository of protein and peptide identifications for the proteomics communityPhilip 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... 
Analysing proteomics identifications in the context of functional and structural protein annotation: integrating annotation using PICR, DAS, and BioMartPhilip Jones
European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK
Methods Mol Biol 696:107-21. 2011....- Using the PRIDE proteomics identifications database for knowledge discovery and data analysisPhilip 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... - PRIDE: new developments and new datasetsPhilip 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... - The Protein Identifier Cross-Referencing (PICR) service: reconciling protein identifiers across multiple source databasesRichard 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... - The Ontology Lookup Service: more data and better tools for controlled vocabulary queriesRichard 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... - Submit your interaction data the IMEx way: a step by step guide to trouble-free depositionSandra 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... - Integrating biological data--the Distributed Annotation SystemAndrew 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... - The PRIDE proteomics identifications database: data submission, query, and dataset comparisonPhilip 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... - Analysis of the experimental detection of central nervous system-related genes in human brain and cerebrospinal fluid datasetsMichael 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... - The Ontology Lookup Service, a lightweight cross-platform tool for controlled vocabulary queriesRichard 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... - Proteomic data exchange and storage: the need for common standards and public repositoriesSandra 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... - InterPro in 2011: new developments in the family and domain prediction databaseSarah 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... - Metagenomic analysis: the challenge of the data bonanzaChris 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... - Proteomics and Beyond: a report on the 3rd Annual Spring Workshop of the HUPO-PSI 21-23 April 2006, San Francisco, CA, USASandra Orchard
EMBL Outstation European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, UK
Proteomics 6:4439-43. 2006.... - ISPIDER Central: an integrated database web-server for proteomicsJennifer 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... - Automated reprocessing pipeline for searching heterogeneous mass spectrometric data of the HUPO Brain Proteome Project pilot phaseChristian Stephan
Medizinisches Proteom Center, Ruhr Universitat Bochum, Bochum, Germany
Proteomics 6:5015-29. 2006.... - PRIDE: the proteomics identifications databaseLennart 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...