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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. Commentary

    Chemical datuments as scientific enablers

    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 ...

    Henry S Rzepa

    Journal of Cheminformatics 2013 5:6

    Published on: 23 January 2013

  2. Research article

    Applied and implied semantics in crystallographic publishing

    Crystallography is a data-rich, software-intensive scientific discipline with a community that has undertaken direct responsibility for publishing its own scientific journals. That community has worked activel...

    Brian McMahon

    Journal of Cheminformatics 2012 4:19

    Published on: 30 August 2012

  3. Software

    Avogadro: an advanced semantic chemical editor, visualization, and analysis platform

    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...

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

    Journal of Cheminformatics 2012 4:17

    Published on: 13 August 2012

  4. Editorial

    Semantic physical science

    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...

    Peter Murray-Rust and Henry S Rzepa

    Journal of Cheminformatics 2012 4:14

    Published on: 3 August 2012