Peter Murray-Rust

Summary

Affiliation: University of Cambridge
Country: UK

Publications

  1. pmc Open bibliography for science, technology, and medicine
    Richard Jones
    Departments of Statistics and Mathematics, University of California, Berkeley, CA, USA
    J Cheminform 3:47. 2011
  2. 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
  3. pmc Bioclipse: an open source workbench for chemo- and bioinformatics
    Ola Spjuth
    Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden
    BMC Bioinformatics 8:59. 2007
  4. pmc Mining chemical information from open patents
    David M Jessop
    Unilever Centre for Molecular Science Informatics, Department of Chemistry, Lensfield Road, Cambridge CB2 1EW, UK
    J Cheminform 3:40. 2011
  5. pmc CMLLite: a design philosophy for CML
    Joe A Townsend
    Unilever Centre for Molecular Science Informatics, Department of Chemistry, Lensfield Road, Cambridge, CB2 1EW, UK
    J Cheminform 3:39. 2011
  6. pmc The Quixote project: Collaborative and Open Quantum Chemistry data management in the Internet age
    Sam Adams
    Unilever Centre for Molecular Science Informatics, Department of Chemistry, Lensfield Road, Cambridge CB2 1EW, UK
    J Cheminform 3:38. 2011
  7. pmc OSCAR4: a flexible architecture for chemical text-mining
    David M Jessop
    Unilever Centre for Molecular Science Informatics, Department of Chemistry, Lensfield Road, Cambridge CB2 1EW, UK
    J Cheminform 3:41. 2011
  8. pmc The semantic architecture of the World-Wide Molecular Matrix (WWMM)
    Peter Murray-Rust
    Unilever Centre for Molecular Science Informatics, Department of Chemistry, Lensfield Road, Cambridge CB2 1EW, UK
    J Cheminform 3:42. 2011
  9. pmc The semantics of Chemical Markup Language (CML): dictionaries and conventions
    Peter Murray-Rust
    Unilever Centre for Molecular Science Informatics, Department of Chemistry, Lensfield Road, Cambridge CB2 1EW, UK
    J Cheminform 3:43. 2011
  10. doi Chemistry for everyone
    Peter Murray-Rust
    Unilever Centre for Molecular Sciences Informatics, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
    Nature 451:648-51. 2008

Collaborators

Detail Information

Publications27

  1. pmc Open bibliography for science, technology, and medicine
    Richard Jones
    Departments of Statistics and Mathematics, University of California, Berkeley, CA, USA
    J Cheminform 3:47. 2011
    ..For this large scale endeavour, the engagement and cooperation of the multiple stakeholders in STM publishing - authors, librarians, publishers and administrators - is sought...
  2. 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:..
  3. pmc Bioclipse: an open source workbench for chemo- and bioinformatics
    Ola Spjuth
    Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden
    BMC Bioinformatics 8:59. 2007
    ..No open source chemoinformatics workbench has previously been published, and no successful attempts have been made to integrate chemo- and bioinformatics into a single framework...
  4. pmc Mining chemical information from open patents
    David M Jessop
    Unilever Centre for Molecular Science Informatics, Department of Chemistry, Lensfield Road, Cambridge CB2 1EW, UK
    J Cheminform 3:40. 2011
    ..NMR spectra reported as product characterisation data are additionally captured...
  5. pmc CMLLite: a design philosophy for CML
    Joe A Townsend
    Unilever Centre for Molecular Science Informatics, Department of Chemistry, Lensfield Road, Cambridge, CB2 1EW, UK
    J Cheminform 3:39. 2011
    ..This article explores the rationale behind the changes which have been made to the schema, explains how conventions interact and how they are designed, formulated, implemented and tested, and gives an overview of the validation service...
  6. pmc The Quixote project: Collaborative and Open Quantum Chemistry data management in the Internet age
    Sam Adams
    Unilever Centre for Molecular Science Informatics, Department of Chemistry, Lensfield Road, Cambridge CB2 1EW, UK
    J Cheminform 3:38. 2011
    ..Not only will these results help to change the data management model in the field of Quantum Chemistry, but the methodology can be applied to other pressing problems related to data in computational and experimental science...
  7. pmc OSCAR4: a flexible architecture for chemical text-mining
    David M Jessop
    Unilever Centre for Molecular Science Informatics, Department of Chemistry, Lensfield Road, Cambridge CB2 1EW, UK
    J Cheminform 3:41. 2011
    ..OSCAR4 offers a domain-independent architecture upon which chemistry specific text-mining tools can be built, and its development and usage are discussed...
  8. pmc The semantic architecture of the World-Wide Molecular Matrix (WWMM)
    Peter Murray-Rust
    Unilever Centre for Molecular Science Informatics, Department of Chemistry, Lensfield Road, Cambridge CB2 1EW, UK
    J Cheminform 3:42. 2011
    ..The technical specification and implementation is now complete. We discuss the types of architecture required to implement nodes in the WWMM and consider the social issues involved in adoption...
  9. pmc The semantics of Chemical Markup Language (CML): dictionaries and conventions
    Peter Murray-Rust
    Unilever Centre for Molecular Science Informatics, Department of Chemistry, Lensfield Road, Cambridge CB2 1EW, UK
    J Cheminform 3:43. 2011
    ..An additional set of conventions and dictionaries are used to support scientific units. All conventions, dictionaries and dictionary elements are identifiable and addressable through unique URIs...
  10. doi Chemistry for everyone
    Peter Murray-Rust
    Unilever Centre for Molecular Sciences Informatics, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
    Nature 451:648-51. 2008
  11. pmc CML: Evolution and design
    Peter Murray-Rust
    Unilever Centre for Molecular Science Informatics, Department of Chemistry, Lensfield Road, Cambridge CB2 1EW, UK
    J Cheminform 3:44. 2011
    ..ABSTRACT: A retrospective view of the design and evolution of Chemical Markup Language (CML) is presented by its original authors...
  12. pmc Ami - The chemist's amanuensis
    Brian J Brooks
    Unilever Centre for Molecular Science Informatics, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
    J Cheminform 3:45. 2011
    ..Investigations suggest that it would not be an ideal device for controlling a mouse, but it shows promise for usages such as manipulating virtual molecules...
  13. pmc Semantic science and its communication - a personal view
    Peter Murray-Rust
    Unilever Centre for Molecular Science Informatics, Department of Chemistry, Lensfield Road, Cambridge CB2 1EW, UK
    J Cheminform 3:48. 2011
    ..They cover a wide range of content, approaches and styles and apart from the selection of the speakers (and hence the authors) I have not exercised any control over the content...
  14. pmc Chemistry in bioinformatics
    Peter Murray-Rust
    Unilever Centre for Molecular Science Informatics, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
    BMC Bioinformatics 6:141. 2005
    ..We argue that the technology is already available; we require a collective agreement to enhance publication protocols...
  15. doi SPECTRa-T: machine-based data extraction and semantic searching of chemistry e-theses
    Jim Downing
    Unilever Centre for Molecular Informatics, Department of Chemistry, Lensfield Rd, Cambridge CB2 1EW, UK
    J Chem Inf Model 50:251-61. 2010
    ..This integrated information has been deposited in a persistent Resource Description Framework (RDF) triple-store that allows users to conduct semantic searches. The strength and weaknesses of several document formats are reviewed...
  16. pmc Communication and re-use of chemical information in bioscience
    Peter Murray-Rust
    Unilever Centre for Molecular Science Informatics, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
    BMC Bioinformatics 6:180. 2005
    ..It is argued that if publishers adopt these tools and protocols, then the quality and quantity of chemical information available to bioscientists will increase and the authors, publishers and readers will find the process cost-effective...
  17. pmc MACiE: a database of enzyme reaction mechanisms
    Gemma L Holliday
    Unilever Centre for Molecular Science Informatics, Department of Chemistry, University of Cambridge Lensfield Road, Cambridge, CB2 1EW, UK
    Bioinformatics 21:4315-6. 2005
    ....
  18. ncbi Chemical documents: machine understanding and automated information extraction
    Joe A Townsend
    Unilever Centre for Molecular Science Informatics, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
    Org Biomol Chem 2:3294-300. 2004
    ..The identification of key units of information, such as chemical names, makes the extraction of useful information from unstructured documents possible...
  19. pmc The semantics of Chemical Markup Language (CML) for computational chemistry : CompChem
    Weerapong Phadungsukanan
    Department of Chemical Engineering and Biotechnology, University of Cambridge, New Museums Site, Pembroke Street, Cambridge, CB2 3RA, UK
    J Cheminform 4:15. 2012
    ..In addition, some of the challenges and difficulties in developing common computational chemistry dictionaries are discussed. The uses of CompChem are illustrated by two practical applications...
  20. doi SPECTRa: the deposition and validation of primary chemistry research data in digital repositories
    Jim Downing
    Unilever Centre for Molecular Informatics, Department of Chemistry, Cambridge University, Lensfield Road, Cambridge, U K
    J Chem Inf Model 48:1571-81. 2008
    ..Context-specific chemical metadata and persistent Handle identifiers are added to enable long-term data reuse. It was found essential to provide an embargo mechanism, and policies for operating this and other processes are presented...
  21. ncbi A global resource for computational chemistry
    Peter Murray-Rust
    Department of Chemistry, Unilever Centre for Molecular Informatics, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
    J Mol Model 11:532-41. 2005
    ..A number of novel features of the PM5 Hamiltonian were identified as a result of the high-throughput approach. The system and the data can be redistributed and reused and promote the value of computed data as a primary chemical resource...
  22. pmc ChemicalTagger: A tool for semantic text-mining in chemistry
    Lezan Hawizy
    Unilever Centre for Molecular Science Informatics, Department of Chemistry, Lensfield Road, Cambridge, CB2 1EW, UK
    J Cheminform 3:17. 2011
    ..abstract:..
  23. doi First-principles thermochemistry for gas phase species in an industrial rutile chlorinator
    Raphael Shirley
    Department of Chemical Engineering and Biotechnology, University of Cambridge, New Museums Site, Cambridge, United Kingdom
    J Phys Chem A 114:11825-32. 2010
    ..Example scripts are provided to demonstrate how to query and retrieve the data automatically...
  24. pmc Semantic physical science
    Peter Murray-Rust
    Department of Chemistry, Imperial College London, Exhibition Road Campus, London, SW7 2AZ, UK
    J Cheminform 4:14. 2012
    ..We invited people who shared our vision for the potential of the web to support chemical and related subjects. Other than the initial invitations, we have not exercised any control over the content of the contributed articles...
  25. pmc MACiE (Mechanism, Annotation and Classification in Enzymes): novel tools for searching catalytic mechanisms
    Gemma L Holliday
    EMBL EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Nucleic Acids Res 35:D515-20. 2007
    ..We also present Version 2 of MACiE, which doubles the dataset available (from Version 1). MACiE can be accessed from http://www.ebi.ac.uk/thornton-srv/databases/MACiE/..
  26. ncbi The Blue Obelisk-interoperability in chemical informatics
    Rajarshi Guha
    Pennsylvania State University, University Park, Pennsylvania 16804 3000, Jmol Project, USA
    J Chem Inf Model 46:991-8. 2006
    ....
  27. ncbi Chemical Markup, XML, and the World Wide Web. 7. CMLSpect, an XML vocabulary for spectral data
    Stefan Kuhn
    Cologne University Bioinformatics Center CUBIC, Cologne, Germany
    J Chem Inf Model 47:2015-34. 2007
    ..The paper describes the CMLElements used and gives practical examples for common types of spectra. In addition it demonstrates how different views of the data can be expressed and what problems still exist...