R Apweiler

Summary

Affiliation: Wellcome Trust Genome Campus
Country: UK

Publications

  1. doi request reprint 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. pmc 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. 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
  4. 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
  5. ncbi request reprint 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. pmc 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 request reprint 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 request reprint 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 request reprint 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. pmc 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

Detail Information

Publications98

  1. doi request reprint 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. pmc 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. 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...
  4. 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...
  5. ncbi request reprint 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. pmc 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 request reprint 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 request reprint 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 request reprint 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. pmc 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. pmc 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 request reprint 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 request reprint 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. doi request reprint 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 request reprint 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. pmc 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. pmc 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 request reprint 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 request reprint 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 request reprint 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
    ..The program varsplic.pl uses information present in the SWISS-PROT and TrEMBL databases to create new records for alternatively spliced isoforms. These new records can be used in similarity searches...
  21. ncbi request reprint 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 request reprint 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...
  23. pmc 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 request reprint 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 request reprint 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 request reprint A collection of well characterised integral membrane proteins
    S Moller
    European Bioinformatics Institute, Cambridge, UK
    Bioinformatics 16:1159-60. 2000
    ..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 request reprint 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 request reprint 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...
  29. pmc 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 request reprint 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. pmc 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 request reprint 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 request reprint Filtering erroneous protein annotation
    D Wieser
    Sequence Database Group, European Bioinformatics Institute, Cambridge, UK
    Bioinformatics 20:i342-7. 2004
    ..We present a post-processing system called Xanthippe that is based on a simple exclusion mechanism and a decision tree approach using the C4.5 data-mining algorithm...
  34. ncbi request reprint 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 request reprint 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. pmc 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. pmc 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 request reprint 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. pmc 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 request reprint 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 request reprint 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...
  42. pmc 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 request reprint 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. 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...
  45. ncbi request reprint 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 request reprint 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 request reprint 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 request reprint 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 request reprint 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. pmc 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. doi request reprint 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. pmc 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. pmc 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 request reprint 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. 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...
  56. ncbi request reprint 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. doi request reprint 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. pmc 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. pmc 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. 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...
  61. ncbi request reprint 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. pmc 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. pmc 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 request reprint 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 request reprint 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 request reprint 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 request reprint 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 request reprint 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. pmc 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. pmc 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. pmc 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. pmc 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 request reprint 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. pmc 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 request reprint 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 request reprint 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 request reprint 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. pmc 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. pmc 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. pmc 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. pmc 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 request reprint 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 request reprint 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 request reprint 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 request reprint 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 request reprint 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 request reprint 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 request reprint 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
    ..InterProScan is designed to be a scalable and extensible system with a robust internal architecture...
  89. pmc 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. pmc 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 request reprint Do you do text?
    Christian Blaschke
    Centro Nacional de Biotecnologia, CNB CSIC Cantoblanco, Madrid, Spain
    Bioinformatics 21:4199-200. 2005
  92. pmc 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 request reprint 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 request reprint 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. pmc 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 request reprint 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 request reprint 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...

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