Visions of a semantic molecular future
Collection published: 14 October 2011
This thematic issue arose from a symposium held in the Unilever Centre [for Molecular Science Informatics, Department of Chemistry, University of Cambridge] on 2011-01-15/17 to celebrate the career of Peter Murray-Rust. From the programme:
This symposium addresses the creativity of the maturing Semantic Web to the unrealized potential of Molecular Science. The world is changing and we are in the middle of many revolutions: Cloud computing; the Semantic Web; the Fourth Paradigm (data-driven science); web democracy; weak AI; pervasive devices; citizen science; Open Knowledge. Technologies can develop in months to a level where individuals and small groups can change the world. However science is hamstrung by archaic approaches to the publication, redistribution and re-use of information and much of the vision is (just) out of reach. Social, as well as technical, advances are required to realize the full potential. We've asked leading scientists to let their imagination explore the possible and show us how to get there.
This is a starting point for all of us - the potential of working with the virtual world of scientists and citizens, coordinated through organizations such as the Open Knowledge Foundation and continuing connection with the Cambridge academic community makes this one of the central points for my future.
The pages in this document represent vibrant communities of practice which are growing and are offered to the world as contributions to a bsemantic molecular future.
We have combined talks from the symposium with work from the Murray-Rust group into 15 articles.
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Semantic science and its communication - a personal view
Peter Murray-Rust Journal of Cheminformatics 2011, 3:48 (14 October 2011)
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Open Bibliography for Science, Technology, and Medicine
Richard Jones, Mark MacGillivray, Peter Murray-Rust, Jim Pitman, Peter Sefton, Ben O'Steen, William Waites Journal of Cheminformatics 2011, 3:47 (14 October 2011)
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Editor’s summary
BibJSON, a simple structured text data format suitable for serialisation and storage of large quantities of bibliographic data is presented and the concept of a distributed bibliography is explored
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The past, present and future of Scientific discourse
Henry S Rzepa Journal of Cheminformatics 2011, 3:46 (14 October 2011)
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Graphical abstract
The increased functionality offered by online publishing is explored by comparing a paper published in 1953 with one from 2010, illustrating how additional data sources can be implemented
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Ami - The chemist's amanuensis
Brian J Brooks, Adam L Thorn, Matthew Smith, Peter Matthews, Shaoming Chen, Ben O'Steen, Sam E Adams, Joe A Townsend, Peter Murray-Rust Journal of Cheminformatics 2011, 3:45 (14 October 2011)
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Graphical abstract
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CML: Evolution and design
Peter Murray-Rust, Henry S Rzepa Journal of Cheminformatics 2011, 3:44 (14 October 2011)
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The semantics of Chemical Markup Language (CML): dictionaries and conventions
Peter Murray-Rust, Joe A Townsend, Sam E Adams, Weerapong Phadungsukanan, Jens Thomas Journal of Cheminformatics 2011, 3:43 (14 October 2011)
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The semantic architecture of the World-Wide Molecular Matrix (WWMM)
Peter Murray-Rust, Sam E Adams, Jim Downing, Joe A Townsend, Yong Zhang Journal of Cheminformatics 2011, 3:42 (14 October 2011)
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OSCAR4: a flexible architecture for chemical text-mining
David M Jessop, Sam E Adams, Egon L Willighagen, Lezan Hawizy, Peter Murray-Rust Journal of Cheminformatics 2011, 3:41 (14 October 2011)
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Mining chemical information from open patents
David M Jessop, Sam E Adams, Peter Murray-Rust Journal of Cheminformatics 2011, 3:40 (14 October 2011)
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CMLLite: a design philosophy for CML
Joe A Townsend, Peter Murray-Rust Journal of Cheminformatics 2011, 3:39 (14 October 2011)
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The Quixote project: Collaborative and Open Quantum Chemistry data management in the Internet age
Sam Adams, Pablo de Castro, Pablo Echenique, Jorge Estrada, Marcus D Hanwell, Peter Murray-Rust, Paul Sherwood, Jens Thomas, Joe Townsend Journal of Cheminformatics 2011, 3:38 (14 October 2011)
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Open Data, Open Source and Open Standards in chemistry: The Blue Obelisk five years on
Noel M O'Boyle, Rajarshi Guha, Egon L Willighagen, Samuel E Adams, Jonathan Alvarsson, Jean-Claude Bradley, Igor V Filippov, Robert M Hanson, Marcus D Hanwell, Geoffrey R Hutchison, Craig A James, Nina Jeliazkova, Andrew SID Lang, Karol M Langner, David C Lonie, Daniel M Lowe, Jérôme Pansanel, Dmitry Pavlov, Ola Spjuth, Christoph Steinbeck, Adam L Tenderholt, Kevin J Theisen, Peter Murray-Rust Journal of Cheminformatics 2011, 3:37 (14 October 2011)
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Editor’s summary
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Graphical abstract
The work carried out by the Blue Obelisk movement over the last five years is described, with a discussion of the current progress and future challenges in Open Data, Open Standards, and Open Source in chemistry
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Openness as infrastructure
John Wilbanks Journal of Cheminformatics 2011, 3:36 (14 October 2011)
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Three stories about the conduct of science: Past, future, and present
Cameron Neylon Journal of Cheminformatics 2011, 3:35 (14 October 2011)
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Adventures in public data
Dan W Zaharevitz Journal of Cheminformatics 2011, 3:34 (14 October 2011)
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