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Semantic physical science

In January 2012 we held an invited workshop (hackathon) and symposium to investigate and formalise the use of semantics in physical sciences (“Semantic Physical Science” or “SPS”). Although the primary concentration is on physical, instrumental and computational chemistry, many of the principles and tools relate to other sciences rich in numeric data. The primary technologies are based on chemical markup language (CML) and, very recently, MathML, and we show that it is possible to create fully semantic declarative scientific objects. The papers in this series represent the outputs of a number of leading groups e.g. CSIRO, PNNL, STFC, Kitware, IUCr, the Blue Obelisk and the Unilever Centre for Molecular Science Informatics (who hosted the meeting.) The papers will be published by the journal asynchronously involving the normal process of peer-review.

The papers in this series represent the outputs of a number of leading groups e.g. CSIRO, PNNL, STFC, Kitware, IUCr, the Blue Obelisk and the Unilever Centre for Molecular Science Informatics (who hosted the meeting.) The papers will be published by the journal asynchronously involving the normal process of peer-review.

We thank the EPSRC for a "Pathways to Impact" award which funded the workshop and also the Cambridge-related article processing charges.

Readers should also consult our earlier thematic series, "Visions of a Semantic Molecular Future", which laid the groundwork last year for much of the basis of the workshop.

Editors: Dr Peter Murray-Rust and Prof Henry Rzepa


  1. Content type: Research article

    Multidisciplinary integrated research requires the ability to couple thediverse sets of data obtained from a range of complex experiments andcomputer simulations. Integrating data requires semantically richinf...

    Authors: Wibe A de Jong, Andrew M Walker and Marcus D Hanwell

    Citation: Journal of Cheminformatics 2013 5:25

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  2. Content type: Commentary

    This article is an attempt to construct a chemical datument as a means of presenting insights into chemical phenomena in a scientific journal. An exploration of the interactions present in a small fragment of ...

    Authors: Henry S Rzepa

    Citation: Journal of Cheminformatics 2013 5:6

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  3. Content type: Software

    The Avogadro project has developed an advanced molecule editor and visualizer designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related area...

    Authors: Marcus D Hanwell, Donald E Curtis, David C Lonie, Tim Vandermeersch, Eva Zurek and Geoffrey R Hutchison

    Citation: Journal of Cheminformatics 2012 4:17

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  4. Content type: Database

    This paper introduces a subdomain chemistry format for storing computational chemistry data called CompChem. It has been developed based on the design, concepts and methodologies of Chemical Markup Language (C...

    Authors: Weerapong Phadungsukanan, Markus Kraft, Joe A Townsend and Peter Murray-Rust

    Citation: Journal of Cheminformatics 2012 4:15

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  5. Content type: Editorial

    The articles in this special issue arise from a workshop and symposium held in January 2012 (Semantic Physical Science’). We invited people who shared our vision for the potential of the web to support chemica...

    Authors: Peter Murray-Rust and Henry S Rzepa

    Citation: Journal of Cheminformatics 2012 4:14

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