H Hermjakob

Summary

Affiliation: Wellcome Trust Genome Campus
Country: UK

Publications

  1. pmc The IntAct molecular interaction database in 2010
    B Aranda
    EMBL Outstation, European Bioinformatics Institute, Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD, UK
    Nucleic Acids Res 38:D525-31. 2010
  2. pmc Critical amino acid residues in proteins: a BioMart integration of Reactome protein annotations with PRIDE mass spectrometry data and COSMIC somatic mutations
    Nelson Ndegwa
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Database (Oxford) 2011:bar047. 2011
  3. pmc Dasty3, a WEB framework for DAS
    Jose M Villaveces
    Protein and Nucleotide Data Group, EMBL Outstation European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Bioinformatics 27:2616-7. 2011
  4. pmc Hydra: a scalable proteomic search engine which utilizes the Hadoop distributed computing framework
    Steven Lewis
    Institute for Systems Biology, Seattle, WA, USA
    BMC Bioinformatics 13:324. 2012
  5. pmc Calling on a million minds for community annotation in WikiProteins
    Barend Mons
    Erasmus Medical Centre, Department of Medical Informatics, Rotterdam, The Netherlands
    Genome Biol 9:R89. 2008
  6. pmc MINT and IntAct contribute to the Second BioCreative challenge: serving the text-mining community with high quality molecular interaction data
    Andrew Chatr-Aryamontri
    Department of Biology, University of Rome, Tor Vergata, Via della Ricerca Scientifica, 00133 Rome, Italy
    Genome Biol 9:S5. 2008
  7. 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
  8. pmc DAS writeback: a collaborative annotation system
    Gustavo A Salazar
    Computer Sciences Department, University of Cape Town, South Africa
    BMC Bioinformatics 12:143. 2011
  9. pmc easyDAS: automatic creation of DAS servers
    Bernat Gel Moreno
    Software Department, UPC BarcelonaTech, Barcelona, Spain
    BMC Bioinformatics 12:23. 2011
  10. 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

Detail Information

Publications84

  1. pmc The IntAct molecular interaction database in 2010
    B Aranda
    EMBL Outstation, European Bioinformatics Institute, Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD, UK
    Nucleic Acids Res 38:D525-31. 2010
    ..Specialized views then allows 'zooming in' on the full annotation of interactions, interactors and their properties. IntAct source code and data are freely available at http://www.ebi.ac.uk/intact...
  2. pmc Critical amino acid residues in proteins: a BioMart integration of Reactome protein annotations with PRIDE mass spectrometry data and COSMIC somatic mutations
    Nelson Ndegwa
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Database (Oxford) 2011:bar047. 2011
    ....
  3. pmc Dasty3, a WEB framework for DAS
    Jose M Villaveces
    Protein and Nucleotide Data Group, EMBL Outstation European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Bioinformatics 27:2616-7. 2011
    ..Dasty3 provides significant improvements on previous Web-based frameworks and is implemented using the 1.6 DAS specification...
  4. pmc Hydra: a scalable proteomic search engine which utilizes the Hadoop distributed computing framework
    Steven Lewis
    Institute for Systems Biology, Seattle, WA, USA
    BMC Bioinformatics 13:324. 2012
    ..Each mass spectrometer can generate data at an astonishingly high rate, and the scope of what is searched for is continually increasing. Therefore solutions for improving our ability to perform these searches are needed...
  5. pmc Calling on a million minds for community annotation in WikiProteins
    Barend Mons
    Erasmus Medical Centre, Department of Medical Informatics, Rotterdam, The Netherlands
    Genome Biol 9:R89. 2008
    ..We call on a 'million minds' to annotate a 'million concepts' and to collect facts from the literature with the reward of collaborative knowledge discovery. The system is available for beta testing at http://www.wikiprofessional.org...
  6. pmc MINT and IntAct contribute to the Second BioCreative challenge: serving the text-mining community with high quality molecular interaction data
    Andrew Chatr-Aryamontri
    Department of Biology, University of Rome, Tor Vergata, Via della Ricerca Scientifica, 00133 Rome, Italy
    Genome Biol 9:S5. 2008
    ..The 2006 BioCreative competition was aimed at evaluating text-mining procedures in comparison with manual annotation of protein-protein interactions...
  7. 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
    ....
  8. pmc DAS writeback: a collaborative annotation system
    Gustavo A Salazar
    Computer Sciences Department, University of Cape Town, South Africa
    BMC Bioinformatics 12:143. 2011
    ..DAS offers a way to distribute and access information but it does not provide domain experts with the mechanisms to participate in the curation process of the available biological entities and their annotations...
  9. pmc easyDAS: automatic creation of DAS servers
    Bernat Gel Moreno
    Software Department, UPC BarcelonaTech, Barcelona, Spain
    BMC Bioinformatics 12:23. 2011
    ..Given the clear advantage that the generalized sharing of relevant biological data is for the research community it would be desirable to facilitate the sharing process...
  10. 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...
  11. pmc OntoDas - a tool for facilitating the construction of complex queries to the Gene Ontology
    Kieran O'Neill
    Central Node, National Bioinformatics Network, Golf Park, Raapenberg Road, Cape Town, South Africa
    BMC Bioinformatics 9:437. 2008
    ..Within the biological domain there is an increasing need for software that facilitates the flexible retrieval of information. OntoDas aims to fulfil this need by allowing the definition of queries by selecting valid ontology terms...
  12. 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...
  13. pmc Integrating biological data--the Distributed Annotation System
    Andrew M Jenkinson
    European Bioinformatics Institute, Hinxton, Cambridge, CB10 1SD, UK
    BMC Bioinformatics 9:S3. 2008
    ..DAS continues to expand its applicability and evolve in response to new challenges facing integrative bioinformatics...
  14. 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
    ....
  15. 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...
  16. ncbi request reprint The HUPO proteomics standards initiative--overcoming the fragmentation of proteomics data
    Henning Hermjakob
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
    Proteomics 6:34-8. 2006
    ..In this article we provide an overview of PSI organisational structure, activities, and current results, as well as ways to get involved in the broad-based, open PSI process...
  17. 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...
  18. ncbi request reprint Rintact: enabling computational analysis of molecular interaction data from the IntAct repository
    Tony Chiang
    EBI EMBL, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Bioinformatics 24:1100-1. 2008
    ..These datasets need to be analyzed by computational methods. Software packages in the statistical environment R provide powerful tools for conducting such analyses...
  19. 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...
  20. 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...
  21. doi request reprint The publication and database deposition of molecular interaction data
    Sandra Orchard
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, United Kingdom
    Curr Protoc Protein Sci . 2010
    ..Which method the author selects is largely dictated by the amount of data to be deposited. In addition, two support protocols describe assignment of unambiguous accession numbers and use of controlled vocabulary terms...
  22. doi request reprint Dasty2, an Ajax protein DAS client
    Rafael C Jimenez
    Proteomics Services Team, European Bioinformatics Institute, EMBL, Hinxton, Cambridge CB10 1SD, UK
    Bioinformatics 24:2119-21. 2008
    ..Dasty2 is a highly interactive web client integrating protein sequence annotations from currently more than 40 sources, using the distributed annotation system (DAS)...
  23. 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...
  24. ncbi request reprint Five years of progress in the Standardization of Proteomics Data 4th Annual Spring Workshop of the HUPO-Proteomics Standards Initiative April 23-25, 2007 Ecole Nationale Supérieure (ENS), Lyon, France
    Sandra Orchard
    EMBL Outstation, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Proteomics 7:3436-40. 2007
    ..Finally the Molecular Interaction group discussed the development of a molecular interaction scoring system with accompanying gold standard data test sets...
  25. doi request reprint 6th HUPO Annual World Congress - Proteomics Standards Initiative Workshop 6-10 October 2007, Seoul, Korea
    Sandra Orchard
    EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Proteomics 8:1331-3. 2008
    ..The session ended with a lively debate on the practical implications these advances will have on daily laboratory work, on submission procedures and the tools which are being developed to assist in these activities...
  26. ncbi request reprint The HUPO proteomics standards initiative--easing communication and minimizing data loss in a changing world
    Sandra Orchard
    EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, UK
    Brief Bioinform 9:166-73. 2008
    ..This article will provide an update on the work of this group, the creation and implementation of these standards and the standards-compliant data repositories being established as result of their efforts...
  27. ncbi request reprint Submit your interaction data the IMEx way: a step by step guide to trouble-free deposition
    Sandra Orchard
    European Bioinformatics Institute, Hinxton, Cambridge, UK
    Proteomics 7:28-34. 2007
    ..This article walks the potential submitter through the various routes by which data may be deposited with the databases and describes the tools which have been developed to assist in this process...
  28. pmc PRIDE: new developments and new datasets
    Philip Jones
    EMBL Outstation, European Bioinformatics Institute EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
    Nucleic Acids Res 36:D878-83. 2008
    ..Collaboration with groups outside the EBI has been fruitful in extending PRIDE, including an approach to encode iTRAQ quantitative data in PRIDE XML...
  29. doi request reprint Data standards and controlled vocabularies for proteomics
    Lennart Martens
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Methods Mol Biol 484:279-86. 2008
    ..We describe the origins and overall concepts behind these standards, as well as the individual efforts that are ongoing in the field of mass spectrometry proteomics and protein interactions...
  30. 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...
  31. doi request reprint The PSI semantic validator: a framework to check MIAPE compliance of proteomics data
    Luisa Montecchi-Palazzi
    European Molecular Biology Laboratory European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, UK
    Proteomics 9:5112-9. 2009
    ..The framework source code and its various applications can be found at http://psidev.info/validator...
  32. pmc A community standard format for the representation of protein affinity reagents
    David E Gloriam
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
    Mol Cell Proteomics 9:1-10. 2010
    ..Further information and documentation are available on the PSI-PAR web site...
  33. doi request reprint Annual spring meeting of the Proteomics Standards Initiative
    Sandra Orchard
    EMBL Outstation European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Proteomics 9:4429-32. 2009
    ....
  34. doi request reprint Second Joint HUPO publication and Proteomics Standards Initiative workshop
    Sandra Orchard
    EMBL Outstation European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Proteomics 9:4426-8. 2009
    ..Most of the specialist journals publishing in this field were represented at the event as well as data providers, databases and the authors of the HUPO-PSI standards documents...
  35. 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...
  36. pmc The Protein Feature Ontology: a tool for the unification of protein feature annotations
    Gabrielle A Reeves
    EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
    Bioinformatics 24:2767-72. 2008
    ..Integration of these methods is needed and so far this has not been possible as there was no common vocabulary available that could be used as a standard language...
  37. doi request reprint ENFIN--A European network for integrative systems biology
    Pascal Kahlem
    EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
    C R Biol 332:1050-8. 2009
    ..The computational work includes the development of a database infrastructure (EnCORE), bioinformatics analysis methods and a novel platform for protein function analysis FuncNet...
  38. ncbi request reprint Annual spring meeting of the Proteomics Standards Initiative 23-25 April 2008, Toledo, Spain
    Sandra Orchard
    EMBL Outstation European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, UK
    Proteomics 8:4168-72. 2008
    ..The accompanying controlled vocabularies are continuing to evolve and a number of standards papers are now being finalised prior to publication...
  39. 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
  40. ncbi request reprint The minimum information required for reporting a molecular interaction experiment (MIMIx)
    Sandra Orchard
    European Molecular Biology Laboratory EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, UK
    Nat Biotechnol 25:894-8. 2007
    ....
  41. 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...
  42. 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...
  43. 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...
  44. 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...
  45. 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
    ....
  46. 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...
  47. 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
    ....
  48. 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...
  49. 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...
  50. 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...
  51. 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...
  52. 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
  53. 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
    ....
  54. ncbi request reprint Entering the implementation era: a report on the HUPO-PSI Fall workshop 25-27 September 2006, Washington DC, USA
    Sandra Orchard
    EMBL Outstation European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Proteomics 7:337-9. 2007
    ..In parallel with this, minimum reporting requirement have been developed and are now maturing to the point where they have been submitted for journal publication after prolonged exposure to community-input via the PSI website...
  55. 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
    ....
  56. 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
    ....
  57. ncbi request reprint Proteomics data validation: why all must provide data
    Lennart Martens
    EMBL Outstation, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Mol Biosyst 3:518-22. 2007
    ..This Opinion attempts to shed some light on some of the underlying issues, and proposes certain guidelines authors can adhere to in order to allow others to validate their findings...
  58. 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...
  59. 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...
  60. 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...
  61. ncbi request reprint The proteomics standards initiative
    Sandra Orchard
    EMBL Outstation, European Bioinformatics Institute, Wellcome Trust, Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Proteomics 3:1374-6. 2003
    ..The Protein-Protein Interactions group expects to publish the Level 1 PSI data exchange format for protein-protein interactions soon and discussions as to the content of Level 2 have been initiated...
  62. ncbi request reprint Human Proteome Organization Proteomics Standards Initiative: data standardization, a view on developments and policy
    Lennart Martens
    European Molecular Biology Laboratory Outstation, The European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Mol Cell Proteomics 6:1666-7. 2007
  63. 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...
  64. ncbi request reprint Annotating the human proteome
    Sandra Orchard
    EMBL The European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom
    Mol Cell Proteomics 4:435-40. 2005
    ..Public domain databases are required to manage and collate this information and present it to the user community in both a human and machine readable manner...
  65. ncbi request reprint The PSI formal document process and its implementation on the PSI website
    Juan Antonio Vizcaino
    EMBL Outstation, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Proteomics 7:2355-7. 2007
    ..We here present the web interface used to support these document processes, and explain briefly how interested parties can participate in the review process. The HUPO-PSI website can be found at http://www.psidev.info...
  66. doi request reprint Tackling quantitation: a report on the annual Spring Workshop of the HUPO-PSI 28-30 March 2010, Seoul, South Korea
    Sandra Orchard
    EMBL Outstation European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Proteomics 10:3062-6. 2010
    ..Work was also undertaken to update the MIAPE guidelines, in response to feedback from the editors of a number of proteomic journals...
  67. ncbi request reprint Proteomic data exchange and storage: the need for common standards and public repositories
    Sandra Orchard
    EMBL Outstation Hinxton, European Bioinformatics Institute, Cambridge, UK
    Methods Mol Biol 367:261-70. 2007
    ..Accompanying controlled vocabularies allow the accurate, while systematic, representation of metadata throughout both schema...
  68. pmc The systematic annotation of the three main GPCR families in Reactome
    Bijay Jassal
    European Bioinformatics Institute, Hinxton, Cambridge CB101SD, UK
    Database (Oxford) 2010:baq018. 2010
    ..Database URL: http://www.reactome.org...
  69. doi request reprint implementing data standards: a report on the HUPOPSI workshop September 2009, Toronto, Canada
    Sandra Orchard
    EMBL Outstation European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Proteomics 10:1895-8. 2010
    ..Finally, the audience participated in a lively debate, discussing both the benefits of these standard formats and issues with their adoption and use in a research environment...
  70. ncbi request reprint Do we want our data raw? Including binary mass spectrometry data in public proteomics data repositories
    Lennart Martens
    Department of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
    Proteomics 5:3501-5. 2005
    ..Finally, some suggestions are made for both immediate and future storage of MS data in public repositories...
  71. pmc The minimum information about a genome sequence (MIGS) specification
    Dawn Field
    Natural Environmental Research Council Centre for Ecology and Hydrology, Oxford OX1 3SR, UK
    Nat Biotechnol 26:541-7. 2008
    ..As part of its wider goals, the GSC also supports improving the 'transparency' of the information contained in existing genomic databases...
  72. ncbi request reprint The HUPO Brain Proteome Project jamboree: centralised summary of the pilot studies
    Michael Hamacher
    Medical Proteom Center, Ruhr Universitat Bochum, Bochum, Germany
    Proteomics 6:1719-21. 2006
    ..The results of the reprocessing were presented and tasks forces were initiated to compile, to interpret and to summarise the data obtained...
  73. ncbi request reprint The Proteomics Identifications Database (PRIDE) and the ProteomExchange Consortium: making proteomics data accessible
    Henning Hermjakob
    Expert Rev Proteomics 3:1-3. 2006
  74. pmc The implications of alternative splicing in the ENCODE protein complement
    Michael L Tress
    Structural Computational Biology Programme, Spanish National Cancer Research Centre, E 28029 Madrid, Spain
    Proc Natl Acad Sci U S A 104:5495-500. 2007
    ....
  75. pmc ISPIDER Central: an integrated database web-server for proteomics
    Jennifer A Siepen
    Faculty of Life Sciences, University of Manchester, M13 9PT, UK
    Nucleic Acids Res 36:W485-90. 2008
    ..This web server offers the first truly integrated access to proteomics repositories and provides a unique service to biologists interested in mass spectrometry-based proteomics...
  76. 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...
  77. ncbi request reprint Data management and preliminary data analysis in the pilot phase of the HUPO Plasma Proteome Project
    Marcin Adamski
    University of Michigan, Ann Arbor, MI 48109 2218, USA
    Proteomics 5:3246-61. 2005
    ..Recommendations of the PPP for future large-scale proteomics endeavors are described...
  78. 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...
  79. ncbi request reprint Overview of the HUPO Plasma Proteome Project: results from the pilot phase with 35 collaborating laboratories and multiple analytical groups, generating a core dataset of 3020 proteins and a publicly-available database
    Gilbert S Omenn
    Internal Medicine, University of Michigan, Ann Arbor, MI 48109 0656, USA
    Proteomics 5:3226-45. 2005
    ....
  80. 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...
  81. doi request reprint InteroPORC: automated inference of highly conserved protein interaction networks
    Magali Michaut
    CEA, iBiTecS, Gif sur Yvette, F 91191, France
    Bioinformatics 24:1625-31. 2008
    ..Thus, interologs are useful for a systematic transfer of protein interaction networks between organisms. However, no standard tool is available so far for that purpose...
  82. ncbi request reprint ProteomeBinders: planning a European resource of affinity reagents for analysis of the human proteome
    Michael J Taussig
    Technology Research Group, The Babraham Institute, Cambridge CB22 3AT, UK
    Nat Methods 4:13-7. 2007
    ..Given the huge diversity of the proteome, the scale of the project is potentially immense but nevertheless feasible in the context of a pan-European or even worldwide coordination...
  83. ncbi request reprint A reagent resource to identify proteins and peptides of interest for the cancer community: a workshop report
    Brian B Haab
    Van Andel Research Institute, Grand Rapids, Michigan 49503, USA
    Mol Cell Proteomics 5:1996-2007. 2006
    ..This workshop report explores various approaches to develop a framework that will most effectively fulfill the needs of the NCI and the cancer research community...
  84. ncbi request reprint Analyzing large-scale proteomics projects with latent semantic indexing
    Sebastian Klie
    Martin Luther University Halle Wittenberg, Halle Saale, Germany
    J Proteome Res 7:182-91. 2008
    ..It is clear from these results that the analysis of large bodies of publicly available proteomics data by noise-tolerant algorithms such as the latent semantic analysis holds great promise and is currently underexploited...