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Visions of a semantic molecular future

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.


  1. Research article

    The semantics of Chemical Markup Language (CML): dictionaries and conventions

    The semantic architecture of CML consists of conventions, dictionaries and units. The conventions conform to a top-level specification and each convention can constrain compliant documents through machine-proc...

    Peter Murray-Rust, Joe A Townsend, Sam E Adams, Weerapong Phadungsukanan and Jens Thomas

    Journal of Cheminformatics 2011 3:43

    Published on: 14 October 2011

  2. Research article

    CMLLite: a design philosophy for CML

    CMLLite is a collection of definitions and processes which provide strong and flexible validation for a document in Chemical Markup Language (CML). It consists of an updated CML schema (schema3), conventions s...

    Joe A Townsend and Peter Murray-Rust

    Journal of Cheminformatics 2011 3:39

    Published on: 14 October 2011

  3. Software

    OSCAR4: a flexible architecture for chemical text-mining

    The Open-Source Chemistry Analysis Routines (OSCAR) software, a toolkit for the recognition of named entities and data in chemistry publications, has been developed since 2002. Recent work has resulted in the ...

    David M Jessop, Sam E Adams, Egon L Willighagen, Lezan Hawizy and Peter Murray-Rust

    Journal of Cheminformatics 2011 3:41

    Published on: 14 October 2011

  4. Research article

    Open Data, Open Source and Open Standards in chemistry: The Blue Obelisk five years on

    The Blue Obelisk movement was established in 2005 as a response to the lack of Open Data, Open Standards and Open Source (ODOSOS) in chemistry. It aims to make it easier to carry out chemistry research by prom...

    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…

    Journal of Cheminformatics 2011 3:37

    Published on: 14 October 2011

  5. Research article

    The past, present and future of Scientific discourse

    The science journal is 346 years old in 2011, having evolved continuously but largely incrementally over that period. Its reinvention for an online presence has largely preserved its previously printed nature,...

    Henry S Rzepa

    Journal of Cheminformatics 2011 3:46

    Published on: 14 October 2011

  6. Research article

    CML: Evolution and design

    A retrospective view of the design and evolution of Chemical Markup Language (CML) is presented by its original authors.

    Peter Murray-Rust and Henry S Rzepa

    Journal of Cheminformatics 2011 3:44

    Published on: 14 October 2011

  7. Research article

    The semantic architecture of the World-Wide Molecular Matrix (WWMM)

    The World-Wide Molecular Matrix (WWMM) is a ten year project to create a peer-to-peer (P2P) system for the publication and collection of chemical objects, including over 250, 000 molecules. It has now been ins...

    Peter Murray-Rust, Sam E Adams, Jim Downing, Joe A Townsend and Yong Zhang

    Journal of Cheminformatics 2011 3:42

    Published on: 14 October 2011

  8. Research article

    The Quixote project: Collaborative and Open Quantum Chemistry data management in the Internet age

    Computational Quantum Chemistry has developed into a powerful, efficient, reliable and increasingly routine tool for exploring the structure and properties of small to medium sized molecules. Many thousands of...

    Sam Adams, Pablo de Castro, Pablo Echenique, Jorge Estrada, Marcus D Hanwell, Peter Murray-Rust, Paul Sherwood, Jens Thomas and Joe Townsend

    Journal of Cheminformatics 2011 3:38

    Published on: 14 October 2011

  9. Research article

    Mining chemical information from open patents

    Linked Open Data presents an opportunity to vastly improve the quality of science in all fields by increasing the availability and usability of the data upon which it is based. In the chemical field, there is ...

    David M Jessop, Sam E Adams and Peter Murray-Rust

    Journal of Cheminformatics 2011 3:40

    Published on: 14 October 2011

  10. Oral presentation

    Adventures in public data

    This article contains the slides and transcript of a talk given by Dan Zaharevitz at the "Visions of a Semantic Molecular Future" symposium held at the University of Cambridge Department of Chemistry on 2011-0...

    Dan W Zaharevitz

    Journal of Cheminformatics 2011 3:34

    Published on: 14 October 2011

  11. Research article

    Ami - The chemist's amanuensis

    The Ami project was a six month Rapid Innovation project sponsored by JISC to explore the Virtual Research Environment space. The project brainstormed with chemists and decided to investigate ways to facilitat...

    Brian J Brooks, Adam L Thorn, Matthew Smith, Peter Matthews, Shaoming Chen, Ben O'Steen, Sam E Adams, Joe A Townsend and Peter Murray-Rust

    Journal of Cheminformatics 2011 3:45

    Published on: 14 October 2011

  12. Editorial

    Semantic science and its communication - a personal view

    The articles in this special issue represent the culmination of about 15 years working with the potential of the web to support chemical and related subjects. The selection of papers arises from a symposium he...

    Peter Murray-Rust

    Journal of Cheminformatics 2011 3:48

    Published on: 14 October 2011

  13. Commentary

    Openness as infrastructure

    The advent of open access to peer reviewed scholarly literature in the biomedical sciences creates the opening to examine scholarship in general, and chemistry in particular, to see where and how novel forms o...

    John Wilbanks

    Journal of Cheminformatics 2011 3:36

    Published on: 14 October 2011

  14. Research article

    Open Bibliography for Science, Technology, and Medicine

    The concept of Open Bibliography in science, technology and medicine (STM) is introduced as a combination of Open Source tools, Open specifications and Open bibliographic data. An Openly searchable and navigab...

    Richard Jones, Mark MacGillivray, Peter Murray-Rust, Jim Pitman, Peter Sefton, Ben O'Steen and William Waites

    Journal of Cheminformatics 2011 3:47

    Published on: 14 October 2011