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Semantic physical science

Edited by: Dr Peter Murray-Rust, Henry Rzepa

Collection published: 3 August 2012

Last updated: 24 May 2013

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.


Research article   Open Access

From data to analysis: linking NWChem and Avogadro with the syntax and semantics of Chemical Markup Language

Wibe A de Jong, Andrew M Walker, Marcus D Hanwell Journal of Cheminformatics 2013, 5:25 (24 May 2013)

Abstract | Provisional PDF | PubMed | Graphical abstract

Commentary   Open Access Highly Accessed

Chemical datuments as scientific enablers

Henry S Rzepa Journal of Cheminformatics 2013, 5:6 (23 January 2013)

Abstract | Full text | PDF | PubMed |  Editor’s summary | Graphical abstract

An attempt to construct a chemical datument as a means of presenting insights into chemical phenomena in a scientific journal is presented, with examples of the use of three software tools, one based on Java, the other two using Javascript and HTML5.

Research article   Open Access

Applied and implied semantics in crystallographic publishing

Brian McMahon Journal of Cheminformatics 2012, 4:19 (30 August 2012)

Abstract | Full text | PDF | PubMed

Software   Open Access Highly Accessed

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

Marcus D Hanwell, Donald E Curtis, David C Lonie, Tim Vandermeersch, Eva Zurek, Geoffrey R Hutchison Journal of Cheminformatics 2012, 4:17 (13 August 2012)

Abstract | Full text | PDF | PubMed |  Editor’s summary | Graphical abstract

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 areas.

Database   Open Access Highly Accessed

The semantics of Chemical Markup Language (CML) for computational chemistry : CompChem

Weerapong Phadungsukanan, Markus Kraft, Joe A Townsend, Peter Murray-Rust Journal of Cheminformatics 2012, 4:15 (7 August 2012)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central

Editorial   Open Access

Semantic physical science

Peter Murray-Rust, Henry S Rzepa Journal of Cheminformatics 2012, 4:14 (3 August 2012)

Abstract | Full text | PDF | PubMed


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