Publications 2001-2010
Articles which are Open or otherwise free to access/download (without registration, subscription or payment) are marked thus: FREE!
N.B. Murray-Rust group members highlighted in bold.
Publications 2011 onwards
Publications 1981-2000
Publications 1980 and earlier
FREE! ICE-Theorem - End to end semantically aware eResearch infrastructure for theses
Authors: Peter Sefton - Jim Downing - Nick Day
Journal: J. Digit. Inf., 2010, 11(1)
First-Principles Thermochemistry for Gas Phase Species in an Industrial Rutile Chlorinator
Authors: Raphael Shirley - Weerapong Phadungsukanan - Markus Kraft - Jim Downing - Nick Day - Peter Murray-Rust
Journal: J. Phys. Chem. A, 2010, 114(43), pp.11825-11832
DOI: 10.1021/jp106795p
FREE! The BioPAX community standard for pathway data sharing
Authors: Emek Demir et al.
Journal: Nature Biotechnology, 2010, 28(9), pp.935-942
DOI: 10.1038/nbt.1666
SPECTRa-T: Machine-Based Data Extraction and Semantic Searching of Chemistry e-Theses
Authors: Jim Downing - Matt Harvey - Peter Morgan - Peter Murray-Rust - Henry Rzepa - Diana Stewart - Alan Tonge - Joe Townsend
Journal: J. Chem. Inf. Model., 2010, 50(2), pp. 251-261
DOI: 10.1021/ci9003688
FREE! Automated analysis and validation of open chemical data
Author: Nick Day
Publication: PhD Thesis, 2009, University of Cambridge
FREE! ChemAxiom – An Ontological Framework for Chemistry in Science
Authors: Nico Adams - Edward Cannon - Peter Murray-Rust
Journal: Nature Precedings, posted 03 September 2009
Towards Lensfield - Data Management, Processing and Semantic Publication for Vernacular e-Science
Authors: Nick Day - Jim Downing - Lezan Hawizy - Nico Adams - Peter Murray-Rust
Journal: e-Science, 2009. e-Science '09. Fifth IEEE International Conference on..., 2009, pp. 352-357
DOI: 10.1109/e-Science.2009.56
CHIC - Converting Hamburgers into Cows
Authors: Joe Townsend - Jim Downing - Peter Murray-Rust
Journal: e-Science, 2009. e-Science '09. Fifth IEEE International Conference on..., 2009, pp. 337-343
DOI: 10.1109/e-Science.2009.54
Chemical Markup, XML and the World-Wide Web. 8. Polymer Markup Language
Authors: Nico Adams - Jerry Winter - Peter Murray-Rust - Henry Rzepa
Journal: J. Chem. Inf. Model., 2008, 48(11), pp.2118-2128
DOI: 10.1021/ci8002123
SPECTRa: The deposition and validation of primary chemistry research data in digital repositories
Authors: Jim Downing - Peter Murray-Rust - Alan Tonge - Peter Morgan - Henry Rzepa - Fiona Cotterill - Nick Day - Matt Harvey
Journal: J. Chem. Inf. Model., 2008, 48(8), pp.1571-1581
DOI: 10.1021/ci7004737
Engineering Polymer Informatics: Towards the Computer-Aided Design of Polymers
Authors: Nico Adams - Peter Murray-Rust
Journal: Macromol. Rapid Commun., 2008, 29(8), pp.615-632,
FREE! Chemistry for everyone
Author: Peter Murray-Rust
Journal: Nature, 2008, 451(7179), pp.648-651
DOI: 10.1038/451648a
XML and Its Application in Chemistry
Authors: Peter Murray-Rust - Henry S. Rzepa
Book: Handbook of Chemoinformatics: From Data to Knowledge in 4 Volumes (ed J. Gasteiger), Wiley-VCH Verlag GmbH, Weinheim, Germany.
DOI: 10.1002/9783527618279.ch16
Author: Peter Murray-Rust
Journal: Serials Review, 2008, 34(1), pp. 52-64
DOI: 10.1016/j.serrev.2008.01.001
FREE! The eCrystals Federation: management and publication of small molecule structure data for all
Authors: Simon J. Coles - Michael B. Hursthouse - Richard A. Stephenson - Peter D. Cliff - Elizabeth Lyon - Manjula Patel - Jim Downing - Peter Murray-Rust
Journal: Acta Cryst., 1998, A64, pp. C626-C627
Annotation of Chemical Named Entities
Authors: Peter Corbett - Colin Batchelor - Simone Teufel
Publication: Proceedings of BioNLP 2007: Biological, translational, and clinical language processing (ACL 2007 workshop) 2007, pp. 57-64.
Automated Analysis and Validation of Chemical Literature
Author: Joe Townsend
Publication: PhD Thesis, 2007, University of Cambridge
Chemical markup, XML, and the world wide web. 7. CMLSpect, an XML vocabulary for spectral data
Authors: Stefan Kuhn - Tobias Helmus - Robert Lancashire - Peter Murray-Rust - Henry Rzepa - Christoph Steinbeck - Egon Willighagen
Journal: J. Chem. Inf. Model., 2007, 47(6), pp. 2015-2034
DOI: 10.1021/ci600531a
FREE! Bioclipse: an open source workbench for chemo- and bioinformatics
Authors: Ola Spjuth - Tobias Helmus - Egon Willighagen - Stefan Kuhn - Martin Eklund - Johannes Wagener - Peter Murray-Rust - Christoph Steinbeck - Jarl Wikberg
Journal: BMC Bioinformatics, 2007, 8, Article Number: 59
Authors: Gemma Holliday - Daniel Almonacid - Gail Bartlett - Noel O'Boyle - James Torrance - Peter Murray-Rust - John Mitchell - Janet Thornton
Journal: Nucleic Acids Research, 2007, 35(SI), pp. D515-D520
DOI: 10.1093/nar/gkl774
FREE! Usable grid infrastructures: practical experiences from the eMinerals project
Authors: M.T. Dove - A.M. Walker - T.O.H. White - R.P. Bruin - K.F. Austen - I. Frame - G.-T. Chiang - Peter Murray-Rust - R.P. Tyer - P.A. Couch- - K. Kleese van Dam - S.C. Parker - A. Marmier - C. Arrouvel
Journal: Proceedings of the UK e-Science All Hands Meeting 2007, pp. 48-55
Mathematics and Scientific Markup
Author: Peter Murray-Rust
Book Series: Lecture Notes in Computer Science: Mathematical Knowledge Managment 2007, Proceedings, 2007, 4573, pp. 128-129
FREE! Cascaded classifiers for confidence-based chemical named entity recognition.
Authors: Peter Corbett - Ann Copestake
Journal: BMC Bioinformatics, 2008, 9(Suppl 11):S4.
DOI: 10.1186/1471-2105-9-S11-S4
Information Delivery in Computational Mineral Science: The eMinerals Data Handling System
Authors: T.O.H. White - M.T. Dove - R.P. Bruin - K.F. Austen - A.M. Walker - E. Artacho - A. Marmier - S.C. Parker - Peter Murray-Rust - A.D. Walkingshaw - P.A. Couch - R.P. Tyer - I.T. Todorov - D.J. Wilson
Journal: e-Science and Grid Computing, 2006. e-Science '06. Second IEEE International Conference on..., 2006, p.59
DOI: 10.1109/E-SCIENCE.2006.261143
Computational Grids for Mid-Sized Collaborative Projects: The eMinerals Experience
Authors: M.T. Dove - T.O.H. White - A.M. Walker - R.P. Bruin - K.F. Austen - E. Artacho - L.A. Sullivan - M. Calleja - M.G. Tucker - R.P. Tyer - P.A. Couch - K. Kleese van Dam - R.J. Allan - I.T. Todorov - C. Chapman - W. Emmerich - A. Marmier - S.C. Parker - M.O. Blanchard - C.R.A. Catlow - Z. Du - N. de Leeuw - G.J. Lewis - V. Alexandrov - M. Alfredsson - J.P. Brodholt - Peter Murray-Rust
Journal: e-Science and Grid Computing, 2006. e-Science '06. Second IEEE International Conference on..., 2006, p.95
DOI: 10.1109/E-SCIENCE.2006.261179
FREE! Anatomy of a grid-enabled molecular simulation study: the compressibility of amorphous silica
Authors: Andrew Walker - Martin Dove - Lucy Sullivan - Kostya Trachenko - Richard Bruin - Toby White - Peter Murray-Rust - Rik Tyer - Philip Couch - Ilian Todorov - William Smith - Kerstin Kleese van Dam
Journal: Proceedings of the UK e-Science All Hands Meeting 2006, pp.653-660
FREE! Application and uses of CML within the eMinerals project
Authors: Toby White - Peter Murray-Rust - Phil Couch - Rik Tyer - Richard Bruin - Ilian Todorov - Dan Wilson - Martin Dove - Kat Austen - Steve Parker
Journal: Proceedings of the UK e-Science All Hands Meeting 2006, pp. 606-613
FREE! Survey of Major Tools and Technologies for Grid-enabled Portal Development
Authors: Xiaoyu Yang - Martin T. Dove - Mark Hayes - Mark Calleja - Ligang He - Peter Murray-Rust
Journal: Proceedings of the UK e-Science All Hands Meeting 2006, pp. 353-356
FREE! Developing lightweight application execution mechanisms in grids
Authors: Ligang He - Martin Dove - Mark Hayes - Peter Murray-Rust - Mark Calleja - Xiaoyu Yang - Victor Mman
Journal: Proceedings of the UK e-Science All Hands Meeting 2006, pp. 201-208
FREE! An architecture for language processing for scientific texts
Authors: Ann Copestake - Peter Corbett - Peter Murray-Rust - C.J. Rupp - Advaith Siddharthan - Simone Teufel - Ben Waldron
Journal: Proceedings of the UK e-Science All Hands Meeting 2006, pp. 614-621
Authors: Martin Dove - Lucy Sullivan - Andrew Walker - Richard Bruin - Toby White - Kostya Trachenko - Peter Murray-Rust - Ilian Todorov - Rik Tyer - Philip Couch - Kerstin Kleese van Dam - William Smith
Journal: Mol. Simul., 2006, 32(12-13), pp. 945-952
DOI: 10.1080/08927020600883293
High-throughput identification of chemistry in life science texts
Authors: Peter Corbett - Peter Murray-Rust
Book Series: Lecture Notes in Computer Science: Computational Life Sciences II, Proceedings, 2006, 4216, pp. 107-118
Classification of enzyme reaction mechanisms
Authors: Noel O'Boyle - Gemma Holliday - Daniel Almonacid - Peter Murray-Rust - John Mitchell - Janet Thornton
Journal: Abstracts of Papers of the American Chemical Society, 2006, 231, Meeting Abstract: 46-CINF
Computational chemistry in XML
Authors: Peter Murray-Rust - Henry Rzepa - Joe Townsend - Dan Wilson
Journal: Abstracts of Papers of the American Chemical Society, 2006, 231, Meeting Abstract: 53-CINF
Chemistry publications in CML
Authors: Peter Corbett - Peter Murray-Rust - Nick Day - Joe Townsend - Henry Rzepa
Journal: Abstracts of Papers of the American Chemical Society, 2006, 231, Meeting Abstract: 55-CINF
Chemical markup, XML, and the world wide web. 6. CMLReact, an XML vocabulary for chemical reactions
Authors: Gemma Holliday - Peter Murray-Rust - Henry Rzepa
Journal: J. Chem. Inf. Model., 2006, 46(1), pp. 145-157
DOI: 10.1021/ci0502698
Blue Obelisk - Interoperability in chemical informatics
Authors: Rajarshi Guha - Michael Howard - Geoffrey Hutchison - Peter Murray-Rust - Henry Rzepa - Christoph Steinbeck - Jörg Wegner - Egon Willighagen
Journal: J. Chem. Inf. Model., 2006, 46(3), pp. 991-998
DOI: 10.1021/ci050400b
XML, Chemical Markup Language (CML) and the Datument
Authors: Peter Murray-Rust - Henry S. Rzepa
Book: The ACS Style Guide: Effective Communication of Scientific Information (3rd edition), 2006, ch. 8 (eds. Anne M. Coghill, Lorrin R. Garson; ISBN10: 0841239991)
FREE! eScience usability: the eMinerals experience
Authors: M.T. Dove - T.O. White - R.P. Bruin - M.G. Tucker - M. Calleja - E. Artacho - Peter Murray-Rust - R.P. Tyer - I. Todorov - R.J. Allan - K. Kleese van Dam - W. Smith - C. Chapman - W. Emmerich - A. Marmier - S.C. Parker - G.J. Lewis - S.M. Hasan - A. Thandavan - V. Alexandrov - M. Blanchard - K. Wright - C.R.A. Catlow - Z. Du - N.H. de Leeuw - M. Alfredsson - G.D. Price - J. Brodholt
Journal: Proceedings of the UK e-Science All Hands Meeting 2005, pp. 30-37
Automatic aggregation of open chemical data
Authors: Nick Day - Peter Murray-Rust - Henry Rzepa - Simon Tyrrell - Yong Zhang
Journal: Abstracts of Papers of the American Chemical Society, 2005, 230, pp. U1010-U1011, Meeting Abstract: 26-CINF
Computational chemistry robots
Authors: Joe Townsend - Peter Murray-Rust - Simon Tyrrell - Yong Zhang
Journal: Abstracts of Papers of the American Chemical Society, 2005, 230, pp. U1311-U1312, Meeting Abstract: 129-COMP
A global resource for computational chemistry
Authors: Peter Murray-Rust - Henry Rzepa - James Stewart - Yong Zhang
Journal: J. Mol. Model., 2005, 11(6), pp. 532-541
DOI: 10.1007/s00894-005-0278-1
FREE! MACiE: a database of enzyme reaction mechanisms
Authors: Gemma Holliday - Gail Bartlett - Daniel Almonacid - Noel O'Boyle - Peter Murray-Rust - Janet Thornton - John Mitchell
Journal: Bioinformatics, 2005,21(23), pp. 4315-4316
DOI: 10.1093/bioinformatics/bti693
FREE! Communication and re-use of chemical information in bioscience
Authors: Peter Murray-Rust - John Mitchell - Henry Rzepa
Journal: BMC Bioinformatics, 2005,6, Article Number: 180
Open access and the Chemical Semantic Web
Authors: Peter Murray-Rust - Henry Rzepa
Journal: Abstracts of Papers of the American Chemical Society, 2005, 229(Part 1), pp. U601-U601 Meeting Abstract: 034-CINF
RDF-based molecular relationships, the Semantic Web and the future of scientific publishing
Authors: Henry Rzepa - O. Casher - Peter Murray-Rust
Journal: Abstracts of Papers of the American Chemical Society, 2005, 229(Part 1), pp. U601-U602 Meeting Abstract: 035-CINF
CML tools and information flow in atomic scale simulations
Authors: J. Wakelin - Peter Murray-Rust - Simon Tyrrell - Yong Zhang - Henry Rzepa - A. García
Journal: Mol. Simulation, 2005, 31(5), pp. 315-322
FREE! Chemistry in Bioinformatics
Authors: Peter Murray-Rust - John Mitchell - Henry Rzepa
Journal: BMC Bioinformatics, 2005, 6, Article Number: 141
Enhancement of the chemical semantic web through the use of InChI identifiers
Authors: - Simon Coles - Nick Day - Peter Murray-Rust - Henry Rzepa - Yong Zhang
Journal: Org. Biomol. Chem., 2005, 3(10), pp. 1832-1834
DOI: 10.1039/b502828k
Representation and Use of Chemistry in the Global Electronic Age
Authors: Peter Murray-Rust - Henry Rzepa - Simon Tyrrell - Yong Zhang
Journal: ChemInform, 2005, 36(15)
FREE! The crystallographic semantic web
Authors: Peter Murray-Rust - Simon Tyrrell - Yong Zhang
Journal: Acta Cryst., 2005, A61, p. C481
FREE! CIF2CML - automatic processing of chemical crystallography in XML/CML
Authors: Peter Murray-Rust - Simon Tyrrell
Journal: Acta Cryst., 2005, A61, p. C109
FREE! The use of XML and CML in Computational Chemistry and Physics Programs
Authors: A. García - Peter Murray-Rust - J. Wakelin
Journal: Proceedings of the UK e-Science All Hands Meeting 2004, pp. 1111-1114
CMLSnap: Animated reaction mechanisms
Authors: Gemma Holliday - John Mitchell - Peter Murray-Rust
Journal: Internet J. Chem., 2004, 7(4), Article Number: 4
Semantic grid computing - The WorldWideMolecularMatrix
Authors: - Yong Zhang - Robert Glen - Peter Murray-Rust - Henry Rzepa - Joe Townsend
Journal: Abstracts of Papers of the American Chemical Society, 2004, 227(Part 1), pp. U682-U682 Meeting Abstract: 032-CINF
Capturing chemistry in XML
Authors: Joe Townsend - Peter Murray-Rust
Journal: Abstracts of Papers of the American Chemical Society, 2004, 227(Part 1), pp. U689-U690 Meeting Abstract: 077-CINF
Representation and use of chemistry in the global electronic age
Authors: Peter Murray-Rust - Henry Rzepa - Simon Tyrrell - Yong Zhang
Journal: Org. Biomol. Chem., 2004, 2(22), pp. 3192-3203
DOI: 10.1039/b410732b
Chemical documents: machine understanding and automated information extraction
Authors: Joe Townsend - Sam Adams - Chris Waudby - Vanessa de Souza - Jonathan Goodman - Peter Murray-Rust
Journal: Org. Biomol. Chem., 2004, 2(22), pp. 3294-3300
DOI: 10.1039/b411033a
Experimental data checker: better information for organic chemists
Authors: Sam Adams - Jonathan Goodman - R.J. Kidd - A.D. McNaught - Peter Murray-Rust - Francis Norton - Joe Townsend - Chris Waudby
Journal: Org. Biomol. Chem., 2004, 2(21), pp. 3067-3070
DOI: 10.1039/b411699m
Authors: Peter Murray-Rust - Henry Rzepa - Mark Williamson - Egon Willighagen
Journal: J. Chem. Inf. Comput. Sci., 2004, 44(2), pp. 462–469
DOI: 10.1021/ci034244p
The Next Big Thing: From Hypermedia to Datuments
Authors: Peter Murray-Rust - Henry S. Rzepa
Journal: J. Digit. Inf., 2004, 5(1)
The INChI as an LSID for molecules in lifescience
Authors: Peter Murray-Rust - Henry Rzepa - Steve Stein
Event: W3C Workshop on Semantic Web for Life Sciences, 27-28 October 2004, Cambridge, Massachusetts USA.
Towards a semantic web for chemistry in lifescience
Authors: Peter Murray-Rust - Henry S. Rzepa
Event: W3C Workshop on Semantic Web for Life Sciences, 27-28 October 2004, Cambridge, Massachusetts USA.
Googling for INChIs; A remarkable method of chemical searching
Authors: Peter Murray-Rust - Henry S. Rzepa - Yong Zhang
Event: W3C Workshop on Semantic Web for Life Sciences, 27-28 October 2004, Cambridge, Massachusetts USA.
Environment from the molecular level: an escience testbed project
Authors: Martin T. Dove - Mark Calleja - Jon Wakelin - Kostya Trachenko - Guillaume Ferlat - Peter Murray-Rust - Nora H. de Leeuw - Zhimei Du - G. David Price - Paul B. Wilson - John P. Brodholt - Maria Alfredsson - Arnaud Marmier - Richard P. Tyer - Lisa J. Blanshard - Robert J. Allan - Kerstin Kleese van Dam - Ilian T. Todorov6 - William Smith - Vassil N. Alexandrov - Gareth J. Lewis - Ashish Thandavan - S. Mehmood Hasan
Journal: Proceedings of the UK e-Science All Hands Meeting 2003, pp. 302-305
A semantic GRID for molecular science
Authors: Peter Murray-Rust - Robert C Glen - Henry S. Rzepa - James J.P. Stewart - Joe A. Townsend - Egon L. Willighagen - Yong Zhang
Journal: Proceedings of the UK e-Science All Hands Meeting 2003, pp. 802-804
Novel applications of XML in chemistry
Author: Peter Murray-Rust
Journal: Abstracts of Papers of the American Chemical Society, 2003, 225(Part 1), pp. U554-U554 Meeting Abstract: 032-CINF
Family of XML languages in chemistry
Authors: Henry Rzepa - Peter Murray-Rust
Journal: Abstracts of Papers of the American Chemical Society, 2003, 225(Part 1), pp. U554-U554 Meeting Abstract: 033-CINF
Classification and computer representation of enzyme reactions. Progress towards the development of macie
Authors: Gemma Holliday - Gail Bartlett - Peter Murray-Rust - Janet Thornton - John Mitchell
Journal: Abstracts of Papers of the American Chemical Society, 2003, 226(Part 1), pp. U306-U306 Meeting Abstract: 099-CINF
Towards the chemical semantic web. An introduction to RSS
Authors: Peter Murray-Rust - Henry Rzepa
Journal: Internet J. Chem., 2003, 6(4), Article Number: 4
Chemical Markup, XML, and the World Wide Web. 4. CML Schema
Authors: Peter Murray-Rust - Henry Rzepa
Journal: J. Chem. Inf. Comput. Sci., 2003, 43(3), pp. 757-772
DOI: 10.1021/ci0256541
Online validation and comparison of molfile and CML molecular atom-connection descriptors
Authors: Georgios Gkoutos - Henry Rzepa - Peter Murray-Rust
Journal: Internet J. Chem., 2003, 6(1), Article Number: 1
Authors: Peter Murray-Rust - Henry S. Rzepa
Journal: OCLC Systems & Services, 2003, 19(4), pp. 162-169
DOI: 10.1108/10650750310698784
FREE! The Semantic Grid of Molecules
Authors: Jürgen Harter - Peter Murray-Rust - Yong Zhang
Journal: Proceedings of the UK e-Science All Hands Meeting 2002, pp. 66-67
Towards the chemical Semantic Web
Authors: Peter Murray-Rust - Henry Rzepa
Journal: Proceedings of the 2002 International Chemical Information Conference, 2002, pp. 127-138
STMML. A markup language for scientific, technical and medical publishing
Authors: Peter Murray-Rust - Henry Rzepa
Journal: Data Science J. , 2002, 1, pp. 128-192
DOI: 10.2481/dsj.1.128
Scientific publications in XML - towards a global knowledge base
Authors: Peter Murray-Rust - Henry S. Rzepa
Journal: Data Science J. , 2002, 1, pp. 84-98
DOI: 10.2481/dsj.1.84
Markup Languages - How to structure chemistry related documents
Authors: Peter Murray-Rust - Henry S. Rzepa
Journal: Chemistry Intl., 2002, 24(4), pp. 9-13
FREE! A new publishing paradigm: STM articles as part of the semantic web
Authors: Henry S. Rzepa - Peter Murray-Rust
Journal: Learned Publishing, 2001, 14(3), pp. 177-182
DOI: 10.1087/095315101750240421
The application of XML languages for integrating molecular resources
Authors: Giorgios Gkoutos - Peter Murray-Rust - Henry Rzepa - C. Viravaidya - Michael Wright
Journal: Internet J. Chem., 2001, 4(12), Article Number: 13
Chemical markup, XML and the World-Wide Web. 2. Information objects and the CMLDOM
Authors: Peter Murray-Rust - Henry Rzepa
Journal: J. Chem. Inf. Comput. Sci., 2001, 41(5), pp. 1113-1123
DOI: 10.1021/ci000404a
Chemical markup, XML, and the World-Wide Web. 3. Toward a signed semantic chemical web of trust
Authors: Giorgios Gkoutos - Peter Murray-Rust - Henry Rzepa - Michael Wright
Journal: J. Chem. Inf. Comput. Sci., 2001, 41(5), pp. 1124-1130
DOI: 10.1021/ci000406v
Universal approach to web-based chemistry using XML and CML
Authors: Peter Murray-Rust - Henry Rzepa - Michael Wright
Journal: Abstracts of Papers of the American Chemical Society, 2001, 221(Part 1), pp. U279-U279 Meeting Abstract: 2-CINF
Development of chemical markup language (CML) as a system for handling complex chemical content
Authors: Peter Murray-Rust - Henry Rzepa - Michael Wright
Journal: New J. Chem., 2001, 25(4), pp. 618-634
DOI: 10.1039/b008780g
A resource for transforming HTML and molfile documents to XML compliant form
Authors: Giorgios Gkoutos - P. Kenway - Peter Murray-Rust - Henry Rzepa - Michael Wright
Journal: Internet J. Chem., 2001, 4(5), Article Number: 5
Virtual education for medicinal chemistry: Early experiences in industrial-academic partnership for continuous learning
Authors: T. Brailsford - C. Burt - J. Calder - M. Davies - C. Edge - Peter Murray-Rust - J. Overington - C. Richardson
Journal: Internet J. Chem., 2001, 4(3), Article number: 3