R Apweiler

Summary

Affiliation: Wellcome Trust Genome Campus
Country: UK

Publications

  1. ncbi UniProtJAPI: a remote API for accessing UniProt data
    Samuel Patient
    The European Bioinformatics Institute, Hinxton, Cambridge CB10 1SD, UK
    Bioinformatics 24:1321-2. 2008
  2. ncbi Broadening the horizon--level 2.5 of the HUPO-PSI format for molecular interactions
    Samuel Kerrien
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    BMC Biol 5:44. 2007
  3. ncbi 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
  4. ncbi 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
  5. ncbi Functional information in SWISS-PROT: the basis for large-scale characterisation of protein sequences
    R Apweiler
    EMBL Outstation, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Brief Bioinform 2:9-18. 2001
  6. ncbi UniProt: the Universal Protein knowledgebase
    Rolf Apweiler
    The EMBL Outstation European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Nucleic Acids Res 32:D115-9. 2004
  7. ncbi Managing core resources for genomics and proteomics
    Rolf Apweiler
    The EMBL Outstation, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Pharmacogenomics 4:343-50. 2003
  8. ncbi Protein sequence databases
    Rolf Apweiler
    The EMBL Outstation The European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Curr Opin Chem Biol 8:76-80. 2004
  9. ncbi Protein sequence annotation in the genome era: the annotation concept of SWISS-PROT+TREMBL
    R Apweiler
    EMBL Outstation the European Bioinformatics Institute, Cambridge, UK
    Proc Int Conf Intell Syst Mol Biol 5:33-43. 1997
  10. ncbi Proteome Analysis Database: online application of InterPro and CluSTr for the functional classification of proteins in whole genomes
    R Apweiler
    EMBL Outstation, The European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
    Nucleic Acids Res 29:44-8. 2001

Research Grants

  1. The UniProt protein sequence and function knowledgebase
    Rolf Apweiler; Fiscal Year: 2007

Detail Information

Publications98

  1. ncbi UniProtJAPI: a remote API for accessing UniProt data
    Samuel Patient
    The European Bioinformatics Institute, Hinxton, Cambridge CB10 1SD, UK
    Bioinformatics 24:1321-2. 2008
    ..These objects contain functional annotations or sequence information associated with a UniProt entry. Here, we briefly describe the UniProtJAPI and demonstrate its usage...
  2. ncbi Broadening the horizon--level 2.5 of the HUPO-PSI format for molecular interactions
    Samuel Kerrien
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    BMC Biol 5:44. 2007
    ....
  3. ncbi 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...
  4. ncbi 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...
  5. ncbi Functional information in SWISS-PROT: the basis for large-scale characterisation of protein sequences
    R Apweiler
    EMBL Outstation, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Brief Bioinform 2:9-18. 2001
    ..However, such an approach is heavily dependent on reliable data sources. The SWISS-PROT protein sequence database plays an essential role here owing to its high level of functional information...
  6. ncbi UniProt: the Universal Protein knowledgebase
    Rolf Apweiler
    The EMBL Outstation European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Nucleic Acids Res 32:D115-9. 2004
    ..The UniProt databases can be accessed online (http://www.uniprot.org) or downloaded in several formats (ftp://ftp.uniprot.org/pub). The scientific community is encouraged to submit data for inclusion in UniProt...
  7. ncbi Managing core resources for genomics and proteomics
    Rolf Apweiler
    The EMBL Outstation, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Pharmacogenomics 4:343-50. 2003
    ..In this review, we will provide examples of the core resources maintained at the EBI and summarize important issues of database management of such resources...
  8. ncbi Protein sequence databases
    Rolf Apweiler
    The EMBL Outstation The European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Curr Opin Chem Biol 8:76-80. 2004
    ..Several the leading protein sequence databases are discussed here, with special emphasis on the databases now provided by the Universal Protein Knowledgebase (UniProt) consortium...
  9. ncbi Protein sequence annotation in the genome era: the annotation concept of SWISS-PROT+TREMBL
    R Apweiler
    EMBL Outstation the European Bioinformatics Institute, Cambridge, UK
    Proc Int Conf Intell Syst Mol Biol 5:33-43. 1997
    ..With this in mind, we are dedicating substantial effort to develop and apply computer methods to enhance the functional information attached to TREMBL entries...
  10. ncbi Proteome Analysis Database: online application of InterPro and CluSTr for the functional classification of proteins in whole genomes
    R Apweiler
    EMBL Outstation, The European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
    Nucleic Acids Res 29:44-8. 2001
    ..The Proteome Analysis Database is accompanied by a program that has been designed to carry out InterPro proteome comparisons for any one proteome against any other one or more of the proteomes in the database...
  11. ncbi Tools and resources for identifying protein families, domains and motifs
    Nicola J Mulder
    The EMBL Outstation, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Genome Biol 3:REVIEWS2001. 2002
    ..This article reviews the tools and resources available on the web for identifying signatures within proteins and discusses how they may be used in the analysis of new or unknown protein sequences...
  12. ncbi Interactive InterPro-based comparisons of proteins in whole genomes
    A Kanapin
    EMBL Outstation, The European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
    Bioinformatics 18:374-5. 2002
    ..The Proteome Analysis Database is accompanied by a program that has been designed to carry out interactive InterPro proteome comparisons for any one proteome against any other one or more of the proteomes in the database...
  13. ncbi The role SWISS-PROT and TrEMBL play in the genome research environment
    V Junker
    EMBL Outstation, The European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, UK
    J Biotechnol 78:221-34. 2000
    ..In taking these steps it is hoped that TrEMBL entries are enhanced with some indication as to what a protein is, could or may be...
  14. ncbi The InterPro database and tools for protein domain analysis
    Nicola J Mulder
    The EMBL Outstation, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Curr Protoc Bioinformatics . 2008
    ..In addition, details on browsing InterPro families and domains of interest using the InterPro Web and sequence retrieval system (SRS) are provided to show users how to get the most from the resource...
  15. ncbi Applications of InterPro in protein annotation and genome analysis
    Margaret Biswas
    EBI, Hinxton, Cambridge, UK
    Brief Bioinform 3:285-95. 2002
    ..In the Proteome Analysis Database, InterPro analyses have been combined with other analyses based on CluSTr, the Gene Ontology (GO) and structural information on the proteins...
  16. ncbi The InterPro database, an integrated documentation resource for protein families, domains and functional sites
    R Apweiler
    EMBL Outstation European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Nucleic Acids Res 29:37-40. 2001
    ..The database is accessible for text- and sequence-based searches at http://www.ebi.ac.uk/interpro/. Questions can be emailed to interhelp@ebi.ac.uk...
  17. ncbi CluSTr: a database of clusters of SWISS-PROT+TrEMBL proteins
    E V Kriventseva
    EMBL Outstation, The European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Nucleic Acids Res 29:33-6. 2001
    ..CluSTr also provides cross-references to HSSP and PDB. The database is available for querying and browsing at http://www.ebi.ac.uk/clustr...
  18. ncbi UniProt archive
    Rasko Leinonen
    EMBL Outstation, The European Bioinformatics Institute (EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Bioinformatics 20:3236-7. 2004
    ..UniParc contains only protein sequences and database cross-references; all other information must be retrieved from the source databases...
  19. ncbi Databases and resources for in silico proteome analysis
    Manuela Pruess
    European Bioinformatics Institute, Hinxton, Cambridge, United Kingdom
    Methods Biochem Anal 49:397-414. 2006
  20. ncbi VARSPLIC: alternatively-spliced protein sequences derived from SWISS-PROT and TrEMBL
    P Kersey
    EMBL Outstation Hinxton, The European Bioinformatics Institute EBI, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
    Bioinformatics 16:1048-9. 2000
    ..These new records can be used in similarity searches. AVAILABILITY: The program is available at ftp://ftp.ebi.ac.uk/pub/software/swissprot/, together with regularly updated output files. CONTACT: pkersey@ebi.ac.uk..
  21. ncbi The human proteomics initiative (HPI)
    C O'Donovan
    EMBL Outstation, The European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, UK CB10 1SD
    Trends Biotechnol 19:178-81. 2001
    ..These various approaches have been integrated to attach, extract and combine as much relevant information as possible to the proteome. This resource should be valuable to users from both research and industry...
  22. ncbi EDITtoTrEMBL: a distributed approach to high-quality automated protein sequence annotation
    S Moller
    European Bioinformatics Institute, Hinxton, UK
    Bioinformatics 15:219-27. 1999
    ..We have implemented a prototype and use it in the production of TrEMBL releases. AVAILABILITY: Upon request...
  23. ncbi InterProScan: protein domains identifier
    E Quevillon
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Nucleic Acids Res 33:W116-20. 2005
    ..O'Reilly Publishers, Sebastopol, CA, http://www.w3.org/TR/soap/] are also available to the users. Various output formats are supported and include text tables, XML documents, as well as various graphs to help interpret the results...
  24. ncbi A novel method for automatic functional annotation of proteins
    W Fleischmann
    The EMBL Outstation The European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Bioinformatics 15:228-33. 1999
    ..To improve this situation, we had to develop a method of automatic annotation that produces highly reliable functional prediction using the language and the syntax of SWISS-PROT...
  25. ncbi Representation of functional information in the SWISS-PROT data bank
    V L Junker
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambs, UK
    Bioinformatics 15:1066-7. 1999
    ..Functional information in SWISS-PROT results, primarily, from assessment of articles reporting characterization. Predicted information is labeled with flags describing the evidence level (e.g. potential, probable, by similarity)...
  26. ncbi A collection of well characterised integral membrane proteins
    S Moller
    European Bioinformatics Institute, Cambridge, UK
    Bioinformatics 16:1159-60. 2000
    ..SUMMARY: A collection of transmembrane proteins with annotated transmembrane regions, for which good experimental evidence exist, was created as a test or training set for algorithms to predict transmembrane regions in proteins...
  27. ncbi Automatic rule generation for protein annotation with the C4.5 data mining algorithm applied on SWISS-PROT
    E Kretschmann
    The EMBL Outstation, The European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Bioinformatics 17:920-6. 2001
    ..To improve this situation automatic tools are needed that support manual annotation, automatically increase the amount of reliable information and help to detect inconsistencies in manually generated annotations...
  28. ncbi The predictive power of the CluSTr database
    Robert Petryszak
    EMBL Outstation Hinxton, The European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
    Bioinformatics 21:3604-9. 2005
    ..We conclude that the CluSTr approach to clustering proteins makes a valuable contribution to traditional protein classifications. AVAILABILITY: http://www.ebi.ac.uk/clustr/...
  29. ncbi The Gene Ontology Annotation (GOA) project: implementation of GO in SWISS-PROT, TrEMBL, and InterPro
    Evelyn Camon
    EMBL Outstation-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
    Genome Res 13:662-72. 2003
    ..This vocabulary has also been applied to the nonredundant proteome sets for all other completely sequenced organisms as well as to proteins from a wide range of organisms where the proteome is not yet complete...
  30. ncbi Clustering and analysis of protein families
    E V Kriventseva
    EMBL Outstation, The European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridgeshire CB10 1SD, Hinxton, UK
    Curr Opin Struct Biol 11:334-9. 2001
    ..InterPro and new developments in the analysis of both the phylogenetic profiles of protein families and domain fusion events improve the prediction of specific functions for numerous proteins...
  31. ncbi The Gene Ontology (GO) database and informatics resource
    M A Harris
    GO-EBI, Hinxton, UK
    Nucleic Acids Res 32:D258-61. 2004
    ..The GO Web resource also provides access to extensive documentation about the GO project and links to applications that use GO data for functional analyses...
  32. ncbi Application of InterPro for the functional classification of the proteins of fish origin in SWISS-PROT and TrEMBL
    M Biswas
    EMBL Outstation, The European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    J Biosci 26:277-84. 2001
    ..The comparisons also show that, based on InterPro families, the trans-species evolution of MHC class I and II molecules in mammals and teleost fish can be recognized...
  33. ncbi Filtering erroneous protein annotation
    D Wieser
    Sequence Database Group, European Bioinformatics Institute, Cambridge, UK
    Bioinformatics 20:i342-7. 2004
    ..AVAILABILITY: The application of the Xanthippe rules can be browsed at http://www.ebi.uniprot.org/..
  34. ncbi Integr8: enhanced inter-operability of European molecular biology databases
    P J Kersey
    The European Bioinformatics Institute, Cambridge, UK
    Methods Inf Med 42:154-60. 2003
    ..The solution of this problem is made more difficult by the absence of universal identifiers for biological entities, and the breadth and variety of available data...
  35. ncbi UniSave: the UniProtKB sequence/annotation version database
    Rasko Leinonen
    EMBL Outstation, The European Bioinformatics Institute (EBI) Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Bioinformatics 22:1284-5. 2006
    ..Unlike the UniProtKB, which contains only the latest Swiss-Prot and TrEMBL entry versions, the UniSave provides access to previous versions of these entries. AVAILABILITY: http://www.ebi.ac.uk/uniprot/unisave..
  36. ncbi Improvements to CluSTr: the database of SWISS-PROT+TrEMBL protein clusters
    E V Kriventseva
    EMBL Outstation-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Nucleic Acids Res 31:388-9. 2003
    ..Links to the relevant structural data in Protein Data Bank (PDB) and Homology derived Secondary Structure of Proteins (HSSP) are also provided...
  37. ncbi IntAct--open source resource for molecular interaction data
    S Kerrien
    EMBL Outstation European Bioinformatics Institute EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
    Nucleic Acids Res 35:D561-5. 2007
    ..IntAct supports and encourages local installations as well as direct data submission and curation collaborations. IntAct source code and data are freely available from http://www.ebi.ac.uk/intact...
  38. ncbi The Integr8 project--a resource for genomic and proteomic data
    Manuela Pruess
    EMBL Outstation - European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
    In Silico Biol 5:179-85. 2005
    ..Customisable statistics data are available from the BioMart application, and pre-prepared data can be downloaded from the FTP site...
  39. ncbi E-MSD: an integrated data resource for bioinformatics
    S Velankar
    Macromolecular Structure Database Group (E-MSD, EMBL Outstation, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Nucleic Acids Res 33:D262-5. 2005
    ..This work was carried out under the 'Structure Integration with Function, Taxonomy and Sequences (SIFTS)' initiative (http://www.ebi.ac.uk/msd-srv/docs/sifts) in the MSD group...
  40. ncbi Consistent integration of non-reliable heterogeneous information resources applied to the annotation of transmembrane proteins
    S Moller
    European Bioinformatics Institute, Cambridge, UK
    Comput Chem 26:41-9. 2001
    ..In this paper we set out to develop a general approach to inconsistency management for information agents. It is implemented as part of the EDITtoTrEMBL system and applied on a large real-world problem in the domain of bioinformatics...
  41. ncbi Removing redundancy in SWISS-PROT and TrEMBL
    C O'Donovan
    EMBL Outstation the European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Bioinformatics 15:258-9. 1999
    ..We developed a strategy to identify the redundancy present within and between SWISS-PROT and TrEMBL and its subsequent removal. AVAILABILITY: The tools mentioned in this paper are available on request...
  42. ncbi EMBL Nucleotide Sequence Database: developments in 2005
    Guy Cochrane
    EMBL Outstation European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
    Nucleic Acids Res 34:D10-5. 2006
    ..New developments, the submission process, data retrieval and access to support are presented in this paper, along with links to sources of further information...
  43. ncbi Linking publication, gene and protein data
    Paul Kersey
    EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Nat Cell Biol 8:1183-9. 2006
    ....
  44. ncbi 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...
  45. ncbi The work of the Human Proteome Organisation's Proteomics Standards Initiative (HUPO PSI)
    Chris F Taylor
    European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge, United Kingdom
    OMICS 10:145-51. 2006
    ....
  46. ncbi Autumn 2005 Workshop of the Human Proteome Organisation Proteomics Standards Initiative (HUPO-PSI) Geneva, September, 4-6, 2005
    Sandra Orchard
    EMBL Outstation European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Proteomics 6:738-41. 2006
    ..Common to all these efforts is the field of protein modifications, and work has been initiated to establish an ontology in this field that can be used by both workers in the field of proteomics and the wider scientific community...
  47. ncbi Evidence standards in experimental and inferential INSDC Third Party Annotation data
    Guy Cochrane
    EMBL Nucleotide Sequence Database, EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
    OMICS 10:105-13. 2006
    ..The data are divided into two tiers: those with experimental evidence and those with inferential evidence. Standards for TPA are detailed and illustrated with the aid of case studies...
  48. 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
    ....
  49. ncbi Bioinformatics database infrastructure for biotechnology research
    Eleanor J Whitfield
    EMBL EBI, Wellcome Trust Genome Campus, Hinxton Hall, Hinxton, Cambs CB10 1SD, UK
    J Biotechnol 124:629-39. 2006
    ..Furthermore, some resources offer integrated views on different types of data, allowing the user to do easy customized queries over large datasets and to compare different types of data...
  50. ncbi EMBL Nucleotide Sequence Database in 2006
    Tamara Kulikova
    EMBL Outstation European Bioinformatics Institute, Wellcome Trust Genome Campus Hinxton, Cambridge, CB10 1SD, UK
    Nucleic Acids Res 35:D16-20. 2007
    ..All available resources can be accessed via the EBI home page at http://www.ebi.ac.uk/. Changes over the past year include changes to the file format, further development of the EMBLCDS dataset and developments to the XML format...
  51. ncbi ASTD: The Alternative Splicing and Transcript Diversity database
    Gautier Koscielny
    European Bioinformatics Institute, European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Genomics 93:213-20. 2009
    ..The ASTD database can be accessed at http://www.ebi.ac.uk/astd...
  52. ncbi QuickGO: a web-based tool for Gene Ontology searching
    David Binns
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB101SD, UK
    Bioinformatics 25:3045-6. 2009
    ..It can be queried online at http://www.ebi.ac.uk/QuickGO. The software for QuickGO is freely available under the Apache 2 licence and can be downloaded from http://www.ebi.ac.uk/QuickGO/installation.html..
  53. ncbi Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project
    Chris F Taylor
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
    Nat Biotechnol 26:889-96. 2008
  54. ncbi Genome Reviews: standardizing content and representation of information about complete genomes
    Peter Sterk
    EMBL Outstation, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
    OMICS 10:114-8. 2006
    ..In this paper, the rationale behind the creation of Genome Reviews, the approach taken in standardizing the data and its representation, and particular issues encountered in doing so are described...
  55. ncbi 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...
  56. ncbi The EMBL Nucleotide Sequence and Genome Reviews Databases
    Peter Sterk
    EMBL Outstation the European Bioinformatics Institute, Welcome Trust Genome Campus, Hinxton, Cambridge, UK
    Methods Mol Biol 406:1-21. 2007
    ..Focusing on plant nucleotide sequences, we demonstrate how these data are accessed, how sequence similarity searches are performed and how we can obtain a wealth of additional information relating to genome sequences using Integr8...
  57. ncbi In silico characterization of proteins: UniProt, InterPro and Integr8
    Nicola Jane Mulder
    EMBL Outstation European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
    Mol Biotechnol 38:165-77. 2008
    ..This article reviews the tools and resources available on the web for single and large-scale protein characterization and whole proteome analysis...
  58. ncbi Priorities for nucleotide trace, sequence and annotation data capture at the Ensembl Trace Archive and the EMBL Nucleotide Sequence Database
    Guy Cochrane
    EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Nucleic Acids Res 36:D5-12. 2008
    ..Priorities are discussed in terms of how reliably information can be captured, the long-term benefits of its capture and the ease with which it can be captured...
  59. ncbi InterPro: the integrative protein signature database
    Sarah Hunter
    EMBL Outstation European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Nucleic Acids Res 37:D211-5. 2009
    ..InterPro data may be accessed either via the web address above, via web services, by downloading files by anonymous FTP or by using the InterProScan search software (http://www.ebi.ac.uk/Tools/InterProScan/)...
  60. ncbi 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...
  61. ncbi The minimum information about a proteomics experiment (MIAPE)
    Chris F Taylor
    The HUPO Proteomics Standards Initiative, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
    Nat Biotechnol 25:887-93. 2007
    ....
  62. ncbi New developments in the InterPro database
    Nicola J Mulder
    EMBL Outstation European Bioinformatics Institute Hinxton, Cambridge, UK
    Nucleic Acids Res 35:D224-8. 2007
    ..ebi.ac.uk/interpro), and for download by anonymous FTP (ftp://ftp.ebi.ac.uk/pub/databases/interpro). The InterProScan search tool is now also available via a web service at http://www.ebi.ac.uk/Tools/webservices/WSInterProScan.html...
  63. ncbi Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads
    Kai Ye
    EMBL Outstation European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Bioinformatics 25:2865-71. 2009
    ..Indel detection using next-gen data is difficult and identification of long structural variations is extremely challenging...
  64. ncbi Human Proteome Organisation Proteomics Standards Initiative. Pre-Congress Initiative
    Sandra Orchard
    EMBL Outstation European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Proteomics 5:4651-2. 2005
    ..The General Proteomics Standards group is now working closely with the Functional Genomics Experiment efforts to define a general standard in which to encode data that will enable a systems biology approach to data analysis...
  65. ncbi The International Protein Index: an integrated database for proteomics experiments
    Paul J Kersey
    EMBL Outstation, The European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
    Proteomics 4:1985-8. 2004
    ..IPI (the International Protein Index) has been developed to address these issues and offers complete nonredundant data sets representing the human, mouse and rat proteomes, built from the Swiss-Prot, TrEMBL, Ensembl and RefSeq databases...
  66. ncbi The Gene Ontology Annotation (GOA) Database--an integrated resource of GO annotations to the UniProt Knowledgebase
    Evelyn Camon
    European Bioinformatics Institute (EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
    In Silico Biol 4:5-6. 2004
  67. ncbi Common interchange standards for proteomics data: Public availability of tools and schema
    Sandra Orchard
    EMBL Outstation, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Proteomics 4:490-1. 2004
    ..A draft XML interchange format for mass spectrometry data has been written and is currently undergoing evaluation whilst work is ongoing to develop a proteomics data integration model, MIAPE...
  68. ncbi The HUPO PSI's molecular interaction format--a community standard for the representation of protein interaction data
    Henning Hermjakob
    European Bioinformatics Institute, EBI Hinxton, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Nat Biotechnol 22:177-83. 2004
    ....
  69. ncbi IntAct: an open source molecular interaction database
    Henning Hermjakob
    European Bioinformatics Institute, Hinxton, Cambridge CB10 1SD, UK
    Nucleic Acids Res 32:D452-5. 2004
    ..All IntAct software, data and controlled vocabularies are available at http://www.ebi.ac.uk/intact...
  70. ncbi IntEnz, the integrated relational enzyme database
    Astrid Fleischmann
    EMBL Outstation European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Nucleic Acids Res 32:D434-7. 2004
    ..IntEnz is supported by NC-IUBMB and contains enzyme data curated and approved by this committee. The database IntEnz is available at http://www.ebi.ac.uk/intenz...
  71. ncbi The Gene Ontology Annotation (GOA) Database: sharing knowledge in Uniprot with Gene Ontology
    Evelyn Camon
    European Bioinformatics Institute EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Nucleic Acids Res 32:D262-6. 2004
    ..Researchers wishing to query or contribute to the GOA project are encouraged to email: goa@ebi.ac.uk...
  72. ncbi The EMBL Nucleotide Sequence Database
    Tamara Kulikova
    EMBL Outstation, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Nucleic Acids Res 32:D27-30. 2004
    ..All available resources can be accessed via the EBI home page at http://www.ebi.ac.uk...
  73. ncbi Further advances in the development of a data interchange standard for proteomics data
    Sandra Orchard
    EMBL Outstation, European Bioinformatics Institute, Hinxton, Cambridge, UK
    Proteomics 3:2065-6. 2003
    ..In collaboration with the American Society for Tests and Measurements, the PSI propose to publish this first draft at the forthcoming HUPO 2nd World Congress in Montreal, 8-11 October 2003...
  74. ncbi The Proteome Analysis database: a tool for the in silico analysis of whole proteomes
    Manuela Pruess
    EMBL Outstation, The European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
    Nucleic Acids Res 31:414-7. 2003
    ..Complete proteome analysis is available for a total of 89 proteome sets. A specifically designed application enables InterPro proteome comparisons for any one proteome against any other one or more of the proteomes in the database...
  75. ncbi High-quality protein knowledge resource: SWISS-PROT and TrEMBL
    Claire O'Donovan
    EMBL Outstation, European Bioinformatics Institute, Hinxton, Cambridge, UK
    Brief Bioinform 3:275-84. 2002
    ....
  76. ncbi InterPro: an integrated documentation resource for protein families, domains and functional sites
    Nicola J Mulder
    EMBL Outstation, European Bioinformatics Institute, Hinxton, Cambridge, UK
    Brief Bioinform 3:225-35. 2002
    ..Each InterPro entry lists all the matches against SWISS-PROT and TrEMBL (2,141,621 InterPro hits from 586,124 SWISS-PROT and TrEMBL protein sequences). The database is freely accessible for text- and sequence-based searches...
  77. ncbi Advances in the development of common interchange standards for proteomic data
    Sandra Orchard
    EMBL Outstation European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Proteomics 4:2363-5. 2004
    ..At a recent workshop in Nice, participants gathered to review the progress made to date and assist in pushing the process still further forward...
  78. ncbi InterPro, progress and status in 2005
    Nicola J Mulder
    EMBL Outstation European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Nucleic Acids Res 33:D201-5. 2005
    ..The database is available for text- and sequence-based searches via a webserver (http://www.ebi.ac.uk/interpro), and for download by anonymous FTP (ftp://ftp.ebi.ac.uk/pub/databases/interpro)...
  79. ncbi An evaluation of GO annotation retrieval for BioCreAtIvE and GOA
    Evelyn B Camon
    European Molecular Biology Laboratory, European Bionformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
    BMC Bioinformatics 6:S17. 2005
    ..Finally, we provide the results of the first inter-annotator agreement study for manual GO curation, as well as an assessment of our current electronic GO annotation strategies...
  80. ncbi The EMBL Nucleotide Sequence Database
    Carola Kanz
    EMBL Outstation, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Nucleic Acids Res 33:D29-33. 2005
    ..g. FASTA and BLAST). Changes over the past year include the removal of the sequence length limit, the launch of the EMBLCDSs dataset, extension of the Sequence Version Archive functionality and the revision of quality rules for TPA data...
  81. ncbi Integr8 and Genome Reviews: integrated views of complete genomes and proteomes
    Paul Kersey
    The EMBL Outstation European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Nucleic Acids Res 33:D297-302. 2005
    ..Integr8 also allows the users to customize their own interactive analysis, and to download both customized and prepared datasets for their own use. Integr8 is available at http://www.ebi.ac.uk/integr8...
  82. ncbi Further steps in standardisation. Report of the second annual Proteomics Standards Initiative Spring Workshop (Siena, Italy 17-20th April 2005)
    Sandra Orchard
    EMBL Outstation European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Proteomics 5:3552-5. 2005
    ....
  83. ncbi Second proteomics standards initiative spring workshop
    Sandra Orchard
    EMBL Outstation - European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Expert Rev Proteomics 2:287-9. 2005
  84. ncbi Current status of proteomic standards development
    Sandra Orchard
    EMBL Outstation, European Bioinformatics Institute, Wellcome Trust, Genome Campus, Hinxton, Cambridge, UK
    Expert Rev Proteomics 1:179-83. 2004
    ..The eXtensible Mark-up Language-MI data interchange format, which allows exchange of molecular interaction data, has already been published and major databases within this field are supplying data downloads in this format...
  85. ncbi Further steps towards data standardisation: the Proteomic Standards Initiative HUPO 3(rd) annual congress, Beijing 25-27(th) October, 2004
    Sandra Orchard
    EMBL Outstation European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Proteomics 5:337-9. 2005
    ..Parallel sessions allowed the three work groups to present their progress to interested parties and to collect feedback from groups already implementing the available formats...
  86. 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
    ....
  87. ncbi Evaluation of methods for the prediction of membrane spanning regions
    S Moller
    EMBL Outstation European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Bioinformatics 17:646-53. 2001
    ..Our results show that TMHMM is currently the best performing transmembrane prediction program...
  88. ncbi InterProScan--an integration platform for the signature-recognition methods in InterPro
    E M Zdobnov
    EMBL Outstation, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Bioinformatics 17:847-8. 2001
    ..ebi.ac.uk/pub/software/unix/iprscan/) and the SRS-basedInterProScan is available upon request. We provide the public web interface (http://www.ebi.ac.uk/interpro/scan.html) as well as email submission server (interproscan@ebi.ac.uk)...
  89. ncbi Plant protein annotation in the UniProt Knowledgebase
    Michel Schneider
    Swiss Institute of Bioinformatics, Centre Medical Universitaire, University of Geneva, 1211 Geneva 4, Switzerland
    Plant Physiol 138:59-66. 2005
    ....
  90. ncbi The Universal Protein Resource (UniProt): an expanding universe of protein information
    Cathy H Wu
    Department of Biochemistry and Molecular Biology, Georgetown University Medical Center, 3900 Reservoir Road, NW, Washington, DC 20057-1414, USA
    Nucleic Acids Res 34:D187-91. 2006
    ..A bibliography mapping service has been added, and an ID mapping service will be available soon. UniProt databases can be accessed online at http://www.uniprot.org or downloaded at ftp://ftp.uniprot.org/pub/databases/...
  91. ncbi Do you do text?
    Christian Blaschke
    Centro Nacional de Biotecnologia, CNB CSIC Cantoblanco, Madrid, Spain
    Bioinformatics 21:4199-200. 2005
  92. ncbi The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003
    Brigitte Boeckmann
    Swiss Institute of Bioinformatics, Centre Medical Universitaire, 1 rue Michel Servet, 1211 Geneva 4, Switzerland
    Nucleic Acids Res 31:365-70. 2003
    ..Researchers are welcome to contribute their knowledge to the scientific community by submitting relevant findings to SWISS-PROT at swiss-prot@expasy.org...
  93. ncbi The Functional Genomics Experiment model (FuGE): an extensible framework for standards in functional genomics
    Andrew R Jones
    School of Computer Science, University of Manchester, Oxford Road, Manchester, M13 9PL, UK
    Nat Biotechnol 25:1127-33. 2007
    ..Such advances are important for transparent data management and mining in functional genomics and systems biology...
  94. 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...
  95. ncbi Integrative annotation of 21,037 human genes validated by full-length cDNA clones
    Tadashi Imanishi
    Integrated Database Group, Biological Information Research Center, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
    PLoS Biol 2:e162. 2004
    ..The H-InvDB platform represents a substantial contribution to resources needed for the exploration of human biology and pathology...
  96. 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
    ....
  97. ncbi A common open representation of mass spectrometry data and its application to proteomics research
    Patrick G A Pedrioli
    Institute for Systems Biology, 1441 North 34 Street, Seattle, Washington 98103-8904, USA
    Nat Biotechnol 22:1459-66. 2004
    ..We have also developed an accompanying suite of supporting programs. We expect that this format will facilitate data management, interpretation and dissemination in proteomics research...

Research Grants1

  1. The UniProt protein sequence and function knowledgebase
    Rolf Apweiler; Fiscal Year: 2007
    ....