Christoph Steinbeck

Summary

Affiliation: Wellcome Trust Genome Campus
Country: UK

Publications

  1. pmc MetaboLights--an open-access general-purpose repository for metabolomics studies and associated meta-data
    Kenneth Haug
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
    Nucleic Acids Res 41:D781-6. 2013
  2. pmc Dovetailing biology and chemistry: integrating the Gene Ontology with the ChEBI chemical ontology
    David P Hill
    Mouse Genome Informatics, The Jackson Laboratory, Bar Harbor, ME 04609, USA
    BMC Genomics 14:513. 2013
  3. pmc New developments on the cheminformatics open workflow environment CDK-Taverna
    Andreas Truszkowski
    Chemoinformatics and Metabolism, European Bioinformatics Institute EBI, Cambridge, UK
    J Cheminform 3:54. 2011
  4. pmc Self-organizing ontology of biochemically relevant small molecules
    Leonid L Chepelev
    Department of Biology, Carleton University, Ottawa, Canada
    BMC Bioinformatics 13:3. 2012
  5. pmc Open Data, Open Source and Open Standards in chemistry: The Blue Obelisk five years on
    Noel M O'Boyle
    Analytical and Biological Chemistry Research Facility, Cavanagh Pharmacy Building, University College Cork, College Road, Cork, CO, Cork, Ireland
    J Cheminform 3:37. 2011
  6. pmc OrChem - An open source chemistry search engine for Oracle(R)
    Mark Rijnbeek
    Cheminformatics and Metabolism, European Bioinformatics Institute EBI, Wellcome Trust Genome Campus, Cambridge, UK
    J Cheminform 1:17. 2009
  7. pmc So what have data standards ever done for us? The view from metabolomics
    Julian L Griffin
    The Department of Biochemistry, Tennis Court Road, University of Cambridge, Cambridge CB2 1GA, UK
    Genome Med 2:38. 2010
  8. pmc A Metadata description of the data in "A metabolomic comparison of urinary changes in type 2 diabetes in mouse, rat, and human."
    Julian L Griffin
    MRC Human Nutrition Research, Elsie Widdowson Laboratory, Fulbourn Road, Cambridge, CB1 9NL, UK
    BMC Res Notes 4:272. 2011
  9. pmc Bioclipse 2: a scriptable integration platform for the life sciences
    Ola Spjuth
    Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden
    BMC Bioinformatics 10:397. 2009
  10. pmc Building blocks for automated elucidation of metabolites: machine learning methods for NMR prediction
    Stefan Kuhn
    Leibniz Institute of Plant Biochemistry, Department of Stress and Developmental Biology, Weinberg 3, 06120 Halle, Germany
    BMC Bioinformatics 9:400. 2008

Collaborators

Detail Information

Publications30

  1. pmc MetaboLights--an open-access general-purpose repository for metabolomics studies and associated meta-data
    Kenneth Haug
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
    Nucleic Acids Res 41:D781-6. 2013
    ..Eight hundred twenty-seven of the metabolites identified in these studies have been mapped to ChEBI. These studies cover a variety of techniques, including NMR spectroscopy and mass spectrometry...
  2. pmc Dovetailing biology and chemistry: integrating the Gene Ontology with the ChEBI chemical ontology
    David P Hill
    Mouse Genome Informatics, The Jackson Laboratory, Bar Harbor, ME 04609, USA
    BMC Genomics 14:513. 2013
    ....
  3. pmc New developments on the cheminformatics open workflow environment CDK-Taverna
    Andreas Truszkowski
    Chemoinformatics and Metabolism, European Bioinformatics Institute EBI, Cambridge, UK
    J Cheminform 3:54. 2011
    ..abstract:..
  4. pmc Self-organizing ontology of biochemically relevant small molecules
    Leonid L Chepelev
    Department of Biology, Carleton University, Ottawa, Canada
    BMC Bioinformatics 13:3. 2012
    ..Clearly, there is a need for the automation of this process, especially for novel chemical entities of biological interest...
  5. pmc Open Data, Open Source and Open Standards in chemistry: The Blue Obelisk five years on
    Noel M O'Boyle
    Analytical and Biological Chemistry Research Facility, Cavanagh Pharmacy Building, University College Cork, College Road, Cork, CO, Cork, Ireland
    J Cheminform 3:37. 2011
    ..abstract:..
  6. pmc OrChem - An open source chemistry search engine for Oracle(R)
    Mark Rijnbeek
    Cheminformatics and Metabolism, European Bioinformatics Institute EBI, Wellcome Trust Genome Campus, Cambridge, UK
    J Cheminform 1:17. 2009
    ..We decided to develop an open source chemistry extension for Oracle, the de facto database platform in the commercial world...
  7. pmc So what have data standards ever done for us? The view from metabolomics
    Julian L Griffin
    The Department of Biochemistry, Tennis Court Road, University of Cambridge, Cambridge CB2 1GA, UK
    Genome Med 2:38. 2010
    ..Here, we examine some of the challenges and potential benefits of further efforts towards data standardization in metabolomics and metabonomics...
  8. pmc A Metadata description of the data in "A metabolomic comparison of urinary changes in type 2 diabetes in mouse, rat, and human."
    Julian L Griffin
    MRC Human Nutrition Research, Elsie Widdowson Laboratory, Fulbourn Road, Cambridge, CB1 9NL, UK
    BMC Res Notes 4:272. 2011
    ..abstract:..
  9. pmc Bioclipse 2: a scriptable integration platform for the life sciences
    Ola Spjuth
    Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden
    BMC Bioinformatics 10:397. 2009
    ..Contemporary biological research integrates neighboring scientific domains to answer complex questions in fields such as systems biology and drug discovery. This calls for tools that are intuitive to use, yet flexible to adapt to new tasks...
  10. pmc Building blocks for automated elucidation of metabolites: machine learning methods for NMR prediction
    Stefan Kuhn
    Leibniz Institute of Plant Biochemistry, Department of Stress and Developmental Biology, Weinberg 3, 06120 Halle, Germany
    BMC Bioinformatics 9:400. 2008
    ..This paper evaluates different statistical and machine learning methods to perform predictions of proton NMR spectra based on data from our open database NMRShiftDB...
  11. pmc OntoQuery: easy-to-use web-based OWL querying
    Ilinca Tudose
    Cheminformatics and Metabolism, European Bioinformatics Institute, Cambridge, UK, Swiss Center for Affective Sciences, University of Geneva, Geneva, Switzerland and Evolutionary Bioinformatics, Swiss Institute of Bioinformatics, Lausanne, Romandy, Switzerland
    Bioinformatics 29:2955-7. 2013
    ..The ChEBI installation, ChEBI OntoQuery, is available at http://www.ebi.ac.uk/chebi/tools/ontoquery. Contact: hastings@ebi.ac.uk...
  12. pmc The Enzyme Portal: a case study in applying user-centred design methods in bioinformatics
    Paula de Matos
    EMBL EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    BMC Bioinformatics 14:103. 2013
    ....
  13. pmc CDK-Taverna: an open workflow environment for cheminformatics
    Thomas Kuhn
    Chemoinformatics and Metabolism, European Bioinformatics Institute, Cambridge, UK
    BMC Bioinformatics 11:159. 2010
    ..To freely support open science based on these data resources, it is desirable for the processing tools to be open source and available for everyone...
  14. pmc Natural product-likeness score revisited: an open-source, open-data implementation
    Kalai Vanii Jayaseelan
    Chemoinformatics and Metabolism, European Bioinformatics Institute EBI, UK
    BMC Bioinformatics 13:106. 2012
    ..In this note, we report an open-source and open-data re-implementation of this scoring system, illustrate its efficiency in ranking small molecules for natural product likeness and discuss its potential applications...
  15. pmc The ChEBI reference database and ontology for biologically relevant chemistry: enhancements for 2013
    Janna Hastings
    Department of Cheminformatics and Metabolism, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, UK
    Nucleic Acids Res 41:D456-63. 2013
    ..Finally, our website and web services have had several enhancements, most notably the provision of a dynamic new interactive graph-based ontology visualization...
  16. pmc The MetaboLights repository: curation challenges in metabolomics
    Reza M Salek
    Wellcome Trust Genome Campus, European Bioinformatics Institute, Cheminformatics and Metabolism, Hinxton, Cambridgeshire CB10 1SD, UK
    Database (Oxford) 2013:bat029. 2013
    ..Here, we describe the MetaboLights curation pipeline, its challenges and its practical application in quality control of complex data depositions. Database URL: http://www.ebi.ac.uk/metabolights...
  17. pmc Rhea--a manually curated resource of biochemical reactions
    Rafael Alcántara
    Chemoinformatics and Metabolism Team, European Bioinformatics Institute, Hinxton, Cambridge CB10 1SD, UK
    Nucleic Acids Res 40:D754-60. 2012
    ..This cross-referencing facilitates the mapping and reconciliation of common reactions and compounds between distinct resources, which is a common first step in the reconstruction of genome scale metabolic networks and models...
  18. pmc The EBI enzyme portal
    Rafael Alcántara
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
    Nucleic Acids Res 41:D773-80. 2013
    ..The fact that these data reside in separate databases makes information discovery cumbersome. The main goal of the portal is to simplify this process for end users...
  19. pmc The chemical information ontology: provenance and disambiguation for chemical data on the biological semantic web
    Janna Hastings
    Chemoinformatics and Metabolism, European Bioinformatics Institute, Hinxton, United Kingdom
    PLoS ONE 6:e25513. 2011
    ..The Chemical Information Ontology is being developed as an open collaborative project. More details, together with a downloadable OWL file, are available at http://code.google.com/p/semanticchemistry/ (license: CC-BY-SA)...
  20. doi request reprint A database for chemical proteomics: ChEBI
    Paula de Matos
    European Bioinformatics Institute, Hinxton, UK
    Methods Mol Biol 803:273-96. 2012
    ..The ChEBI database also provides a central reference point in which to access a variety of bioinformatics data points such as pathways and their biochemical reactions; expression data; protein sequence and structures...
  21. pmc Chemical Entities of Biological Interest: an update
    Paula de Matos
    Chemoinformatics and Metabolism Team, European Bioinformatics Institute, Hinxton, Cambridge CB10 1SD, UK
    Nucleic Acids Res 38:D249-54. 2010
    ....
  22. pmc LipidHome: a database of theoretical lipids optimized for high throughput mass spectrometry lipidomics
    Joseph M Foster
    EMBL Outstation, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
    PLoS ONE 8:e61951. 2013
    ..The web application encompasses a browser for viewing lipid records and a 'tools' section where an MS1 search engine is currently implemented. LipidHome can be accessed at http://www.ebi.ac.uk/apweiler-srv/lipidhome...
  23. pmc KNIME-CDK: Workflow-driven cheminformatics
    Stephan Beisken
    European Molecular Biology Laboratory European Bioinformatics Institute EMBL EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    BMC Bioinformatics 14:257. 2013
    ..A workflow-based cheminformatics tool provides the advantage of ease-of-use and interoperability between complementary cheminformatics packages within the same framework, hence facilitating the analysis process...
  24. pmc Bioinformatics meets user-centred design: a perspective
    Katrina Pavelin
    EMBL EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
    PLoS Comput Biol 8:e1002554. 2012
    ..Our aim is to introduce the reader to how selected UCD techniques may be successfully applied to software design for bioinformatics...
  25. pmc Dissemination of metabolomics results: role of MetaboLights and COSMOS
    Reza M Salek
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
    Gigascience 2:8. 2013
    ..COSMOS aims to link life science e-infrastructures within the worldwide metabolomics community as well as develop and maintain open source exchange formats for raw and processed data, ensuring better flow of metabolomics information...
  26. ncbi request reprint Accessing and using chemical property databases
    Janna Hastings
    European Bioinformatics Institute, Hinxton, UK
    Methods Mol Biol 929:193-219. 2012
    ....
  27. pmc Structure-based classification and ontology in chemistry
    Janna Hastings
    Cheminformatics and Metabolism, European Bioinformatics Institute, Hinxton, UK
    J Cheminform 4:8. 2012
    ..abstract:..
  28. pmc Building blocks for automated elucidation of metabolites: natural product-likeness for candidate ranking
    Kalai Vanii Jayaseelan
    Cheminformatics and Metabolism, European Molecular Biology Laboratory European Bioinformatics Institute EMBL EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    BMC Bioinformatics 15:234. 2014
    ....
  29. pmc Metingear: a development environment for annotating genome-scale metabolic models
    John W May
    Cheminformatics and Metabolism, European Molecular Biology Laboratory European Bioinformatics Institute EMBL EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Bioinformatics 29:2213-5. 2013
    ..Annotated models can be exported to the Systems Biology Markup Language open interchange format...