Richard Cote

Summary

Affiliation: Wellcome Trust Genome Campus
Country: UK

Publications

  1. pmc OLS dialog: an open-source front end to the ontology lookup service
    Harald Barsnes
    Department of Informatics, University of Bergen, Bergen, Norway
    BMC Bioinformatics 11:34. 2010
  2. 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
  3. 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
  4. pmc The Ontology Lookup Service: bigger and better
    Richard Cote
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, CB10 1SD, UK
    Nucleic Acids Res 38:W155-60. 2010
  5. 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
  6. pmc A guide to the Proteomics Identifications Database proteomics data repository
    Juan Antonio Vizcaino
    EMBL Outstation, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Proteomics 9:4276-83. 2009
  7. pmc The Proteomics Identifications database: 2010 update
    Juan Antonio Vizcaino
    EMBL Outstation, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Nucleic Acids Res 38:D736-42. 2010
  8. doi request reprint PRIDE: Data submission and analysis
    Juan Antonio Vizcaino
    European Molecular Biology Laboratory European Bioinformatics Institute, Hinxton, Cambridge, United Kingdom
    Curr Protoc Protein Sci . 2010
  9. doi request reprint Using the Proteomics Identifications Database (PRIDE)
    Lennart Martens
    EMBL EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge
    Curr Protoc Bioinformatics . 2008
  10. doi request reprint 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

Detail Information

Publications12

  1. pmc OLS dialog: an open-source front end to the ontology lookup service
    Harald Barsnes
    Department of Informatics, University of Bergen, Bergen, Norway
    BMC Bioinformatics 11:34. 2010
    ..However, finding the correct controlled vocabulary terms can sometimes be a difficult task for the end user annotating these data...
  2. 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...
  3. 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...
  4. pmc The Ontology Lookup Service: bigger and better
    Richard Cote
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, CB10 1SD, UK
    Nucleic Acids Res 38:W155-60. 2010
    ..In addition, newly released software packages now provide easy means to fully integrate OLS functionality in external applications...
  5. 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...
  6. pmc A guide to the Proteomics Identifications Database proteomics data repository
    Juan Antonio Vizcaino
    EMBL Outstation, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Proteomics 9:4276-83. 2009
    ..Finally, we speak about future plans and the role of PRIDE in the ProteomExchange consortium...
  7. pmc The Proteomics Identifications database: 2010 update
    Juan Antonio Vizcaino
    EMBL Outstation, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Nucleic Acids Res 38:D736-42. 2010
    ..Finally, we highlight the importance of data sharing in the proteomics field, and the corresponding integration of PRIDE with other databases in the ProteomExchange consortium...
  8. doi request reprint PRIDE: Data submission and analysis
    Juan Antonio Vizcaino
    European Molecular Biology Laboratory European Bioinformatics Institute, Hinxton, Cambridge, United Kingdom
    Curr Protoc Protein Sci . 2010
    ..Finally, to demonstrate the potential of PRIDE as a source for data mining, an example protocol is provided to showcase the powerful cross-domain query capabilities available through a combination of BioMarts...
  9. doi request reprint Using the Proteomics Identifications Database (PRIDE)
    Lennart Martens
    EMBL EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge
    Curr Protoc Bioinformatics . 2008
    ..This unit describes in detail the functionality that PRIDE provides with regards to searching, viewing, and comparing the available data, as well as different options for submitting data to PRIDE...
  10. doi request reprint 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...
  11. doi request reprint 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...
  12. doi request reprint PRIDE and "Database on Demand" as valuable tools for computational proteomics
    Juan Antonio Vizcaino
    European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK
    Methods Mol Biol 696:93-105. 2011
    ..Additionally, in order to show the potential of PRIDE as a source for data mining, we also explore complex queries using federated BioMart queries to integrate PRIDE data with other resources, such as Ensembl, Reactome, or UniProt...