Sandra Orchard

Summary

Affiliation: Wellcome Trust Genome Campus
Country: UK

Publications

  1. doi request reprint Debunking minimum information myths: one hat need not fit all
    Sandra Orchard
    EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, UK
    N Biotechnol 25:171-2. 2009
  2. pmc The IntAct molecular interaction database in 2012
    Samuel Kerrien
    EMBL Outstation, European Bioinformatics Institute, Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD, UK
    Nucleic Acids Res 40:D841-6. 2012
  3. doi request reprint Data standardization and sharing-the work of the HUPO-PSI
    Sandra Orchard
    EMBL Outstation, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK Electronic address
    Biochim Biophys Acta 1844:82-7. 2014
  4. doi request reprint Molecular interaction databases
    Sandra Orchard
    EMBL Outstation European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Proteomics 12:1656-62. 2012
  5. pmc Protein interaction data curation: the International Molecular Exchange (IMEx) consortium
    Sandra Orchard
    European Molecular Biology Laboratory European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, UK
    Nat Methods 9:345-50. 2012
  6. 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
  7. 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
  8. ncbi request reprint Publication Committee meeting. HUPO 5th annual World Congress. Long Beach, CA, USA 30 October 2006
    Sandra Orchard
    EMBL Outstation European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, UK
    Proteomics 7:1009-11. 2007
  9. ncbi request reprint The HUPO pre-congress Proteomics Standards Initiative workshop. HUPO 5th annual World Congress. Long Beach, CA, USA 28 October-1 November 2006
    Sandra Orchard
    EMBL Outstation European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, UK
    Proteomics 7:1006-8. 2007
  10. 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

Detail Information

Publications68

  1. doi request reprint Debunking minimum information myths: one hat need not fit all
    Sandra Orchard
    EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, UK
    N Biotechnol 25:171-2. 2009
    ..This response is an attempt to set the record straight and ensure that other groups are not discouraged from using these standards or from joining in their further development in either existing or novel areas of research...
  2. pmc The IntAct molecular interaction database in 2012
    Samuel Kerrien
    EMBL Outstation, European Bioinformatics Institute, Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD, UK
    Nucleic Acids Res 40:D841-6. 2012
    ..IntAct is an active contributor to the IMEx consortium (http://www.imexconsortium.org). IntAct source code and data are freely available at http://www.ebi.ac.uk/intact...
  3. doi request reprint Data standardization and sharing-the work of the HUPO-PSI
    Sandra Orchard
    EMBL Outstation, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK Electronic address
    Biochim Biophys Acta 1844:82-7. 2014
    ..This article is part of a Special Issue entitled: Computational Proteomics in the Post-Identification Era. Guest Editors: Martin Eisenacher and Christian Stephan. ..
  4. doi request reprint Molecular interaction databases
    Sandra Orchard
    EMBL Outstation European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Proteomics 12:1656-62. 2012
    ....
  5. pmc Protein interaction data curation: the International Molecular Exchange (IMEx) consortium
    Sandra Orchard
    European Molecular Biology Laboratory European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, UK
    Nat Methods 9:345-50. 2012
    ..We discuss the advantages of such a service to the user, our quality-control measures and our data-distribution practices...
  6. 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...
  7. 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
    ....
  8. ncbi request reprint Publication Committee meeting. HUPO 5th annual World Congress. Long Beach, CA, USA 30 October 2006
    Sandra Orchard
    EMBL Outstation European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, UK
    Proteomics 7:1009-11. 2007
    ..Discussions centred on how best to structure interactions between journals, databases and researchers to improve accessibility to data, and facilitate comparisons between datasets...
  9. ncbi request reprint The HUPO pre-congress Proteomics Standards Initiative workshop. HUPO 5th annual World Congress. Long Beach, CA, USA 28 October-1 November 2006
    Sandra Orchard
    EMBL Outstation European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, UK
    Proteomics 7:1006-8. 2007
    ..This should be achieved by early in 2007...
  10. 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...
  11. 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...
  12. ncbi request reprint HUPO Publications Committee Meeting: 21 April 2006, San Francisco, CA, USA
    Sandra Orchard
    EMBL Outstation European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, UK
    Proteomics 6:4436-8. 2006
    ..The current status of data formats and reporting requirements was reviewed and the attendees agreed that the use of data standards was essential as the field of proteomics grows and matures...
  13. 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...
  14. ncbi request reprint Proteomics: from technology development to biomarker applications
    Sandra Orchard
    EMBL European Bioinformatics Institute, Wellcome Trust, Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
    Expert Rev Proteomics 4:709-10. 2007
  15. 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...
  16. 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
    ....
  17. doi request reprint HUPO World Congress Publication Committee meeting. August 2008, Amsterdam, The Netherlands
    Sandra Orchard
    EMBL Outstation European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Proteomics 9:502-3. 2009
    ..Delegates from industry, academia and the publishing houses discussed how best to bring these bodies closer to together and facilitate the publication process for the bench scientist...
  18. 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...
  19. doi request reprint Managing the data explosion. A report on the HUPO-PSI Workshop. August 2008, Amsterdam, The Netherlands
    Sandra Orchard
    EMBL Outstation European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Proteomics 9:499-501. 2009
    ..Community input on this initiative was requested. Finally, the impact these new data standards are having on the data submission process, which increasingly is an integral part of the publication process, was reviewed and discussed...
  20. ncbi request reprint Minimum information about a bioactive entity (MIABE)
    Sandra Orchard
    EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SD, UK
    Nat Rev Drug Discov 10:661-9. 2011
    ....
  21. 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...
  22. 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...
  23. 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...
  24. 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...
  25. 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...
  26. ncbi request reprint Kinases as targets: prospects for chronic therapy
    Sandra Orchard
    EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
    Curr Opin Drug Discov Devel 5:713-7. 2002
    ....
  27. 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
  28. 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
    ....
  29. 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...
  30. 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...
  31. 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
    ....
  32. 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...
  33. 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
    ....
  34. 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...
  35. 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
    ....
  36. 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...
  37. 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...
  38. ncbi request reprint The MIntAct project--IntAct as a common curation platform for 11 molecular interaction databases
    Sandra Orchard
    European Molecular Biology Laboratory, European Bioinformatics Institute EMBL EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK, School of Animal and Comparative Biomedical Sciences, The University of Arizona, Tucson, AZ 85721 0036, USA, Swiss Prot group, SIB Swiss Institute of Bioinformatics, CMU, 1 rue Michel Servet, CH 1211 Geneva 4, Switzerland, Department of Biology, University of Rome Tor Vergata, Rome 00133, Italy, Ontario Cancer Institute, The Campbell Family Institute for Cancer Research, and Techna Institute, University Health Network, Toronto, Ontario M5G 0A3, Canada, Cardiovascular Gene Annotation Initiative, Centre for Cardiovascular Genetics, Institute of Cardiovascular Science, University College London, London WC1E 6BT, UK, Centre for Microbial Diseases and Immunity Research, University of British Columbia, Vancouver, British Columbia V6T 1Z4 Canada, Mechanobiology Institute, National University of Singapore, T Lab 05 01, 5A Engineering Drive 1, Singapore 117411, Singapore, Department of Cancer Research and Molecular Medicine, India
    Nucleic Acids Res 42:D358-63. 2014
    ..Both IntAct and MINT are active contributors to the IMEx consortium (http://www.imexconsortium.org). ..
  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 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...
  41. 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)...
  42. 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...
  43. doi request reprint Preparing to work with big data in proteomics - a report on the HUPO-PSI Spring Workshop: April 15-17, 2013, Liverpool, UK
    Sandra Orchard
    European Bioinformatics Institute EMBL EBI, European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Proteomics 13:2931-7. 2013
    ..Finally, the group engaged in discussion on how the existing work of the HUPO-PSI can be leveraged by the Metabolomics Standards Initiative to improve the capture of metabolite data...
  44. doi request reprint A new reference implementation of the PSICQUIC web service
    Noemi Del-Toro
    EMBL European Bioinformatics Institute, Hinxton, Cambridge CB10 1SD, UK
    Nucleic Acids Res 41:W601-6. 2013
    ..This application is free and open to all users with no login requirement (http://www.ebi.ac.uk/Tools/webservices/psicquic/view/main.xhtml). ..
  45. 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
  46. 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...
  47. 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...
  48. doi request reprint Ten years of standardizing proteomic data: a report on the HUPO-PSI Spring Workshop: April 12-14th, 2012, San Diego, USA
    Sandra Orchard
    EMBL Outstation European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Proteomics 12:2767-72. 2012
    ....
  49. doi request reprint From proteomics data representation to public data flow: a report on the HUPO-PSI workshop September 2011, Geneva, Switzerland
    Sandra Orchard
    EMBL Outstation European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Proteomics 12:351-5. 2012
    ..Finally, the ProteomeXchange Consortium, which will supply a single entry point for the submission of MS proteomics data to multiple data resources including PRIDE and PeptideAtlas, is currently being established...
  50. 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...
  51. pmc From protein sequences to 3D-structures and beyond: the example of the UniProt knowledgebase
    Ursula Hinz
    Swiss Prot group, Swiss Institute of Bioinformatics, 1 rue Michel Servet, 1211, Geneva, Switzerland
    Cell Mol Life Sci 67:1049-64. 2010
    ..uniprot.org/ ). It also evokes precautions that are necessary for successful predictions and extrapolations...
  52. pmc Capturing cooperative interactions with the PSI-MI format
    Kim Van Roey
    Structural and Computational Biology Unit, European Molecular Biology Laboratory EMBL, Meyerhofstrasse 1, D 69117 Heidelberg, Germany, Proteomics Services, EMBL Outstation, European Bioinformatics Institute EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK and UMR 5086 CNRS Université Lyon 1, Institut de Biologie et Chimie des Proteines, 7 passage du Vercors, 69367 Lyon Cedex 07, France
    Database (Oxford) 2013:bat066. 2013
    ..This will facilitate the storage, exchange and analysis of cooperative interaction data, which in turn will advance experimental research on this fundamental principle in biology...
  53. doi request reprint Enabling BioSharing - a report on the Annual Spring Workshop of the HUPO-PSI April 11-13, 2011, EMBL-Heidelberg, Germany
    Sandra Orchard
    EMBL Outstation European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Proteomics 11:4284-90. 2011
    ....
  54. 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...
  55. doi request reprint Molecular interactions and data standardisation
    Sandra Orchard
    EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Methods Mol Biol 604:309-18. 2010
    ..Finally, tools and frameworks have been created based on PSI-MI standards to facilitate the visualisation and analysis of molecular interaction data...
  56. 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...
  57. pmc Towards BioDBcore: a community-defined information specification for biological databases
    Pascale Gaudet
    Swiss Institute of Bioinformatics, CMU, 1 rue Michel Servet, 1211 Geneva 4, Switzerland
    Nucleic Acids Res 39:D7-10. 2011
    ..BioDBCore will make it easier for users to evaluate the scope and relevance of available resources. This new resource will increase the collective impact of the information present in biological databases...
  58. 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...
  59. doi request reprint Data standardization by the HUPO-PSI: how has the community benefitted?
    Sandra Orchard
    European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK
    Methods Mol Biol 696:149-60. 2011
    ....
  60. 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...
  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. doi request reprint Omics technologies, data and bioinformatics principles
    Maria V Schneider
    EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Methods Mol Biol 719:3-30. 2011
    ..Finally we address the integration of Omics data, and provide several useful links for bioinformatics and Omics...
  63. doi request reprint Preparing molecular interaction data for publication
    Sandra Orchard
    EMBL Outstation, European Bioinformatics Institute EBI, Cambridge, UK
    Methods Mol Biol 694:229-36. 2011
    ..This chapter acts as a brief guide to preparing both large- and small-scale data for publication and gives a range of different submission options...
  64. pmc BioJS: an open source JavaScript framework for biological data visualization
    John Gomez
    European Bioinformatics Institute, Hinxton, Cambridge, UK
    Bioinformatics 29:1103-4. 2013
    ..In addition to the programming framework, BioJS provides a centralized repository of components available for reutilization by the bioinformatics community. Availability and implementation: http://code.google.com/p/biojs/...
  65. 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
    ....
  66. doi request reprint Charting plant interactomes: possibilities and challenges
    Mustafa Morsy
    Department of Biochemistry and Molecular Biology, MS200, University of Nevada, Reno, NV 89557, USA
    Trends Plant Sci 13:183-91. 2008
    ..Bioinformatics approaches for curating and assessing the confidence of these datasets through inter-species comparisons will be crucial in achieving a complete understanding of protein interaction networks in plants...
  67. pmc The annotation of both human and mouse kinomes in UniProtKB/Swiss-Prot: one small step in manual annotation, one giant leap for full comprehension of genomes
    Silvia Braconi Quintaje
    Swiss Prot group, Swiss Institute of Bioinformatics, CMU, 1 Michel Servet, 1211 Geneva 4, Switzerland
    Mol Cell Proteomics 7:1409-19. 2008
    ....