The Semantics of Chemical Markup Language (CML) for Computational Chemistry : CompChem Preprint Cambridge Centre for Computational Chemical Engineering ISSN 1473 { 4273 The Semantics of Chemical Markup Language (CML) for Computational Chemistry : CompChem Weerapong Phadungsukanan 1, Markus Kraft 1, Joe Townsend 2, Peter Murray-Rust 2 released: May 22, 2012 1 Department of Chemical Engineering and 2 Department of Chemistry Biotechnology University of Cambridge University of Cambridge Lensfield Road New Museums Site Cambridge, CB2 1EW Pembroke Street UK Cambridge, CB2 3RA UK E-mail:
[email protected] Preprint No. 117 Keywords: CML, CompChem, RDF, computational chemistry, thermochemistry, control vocab- ulary, rule-based validation Edited by Computational Modelling Group Department of Chemical Engineering and Biotechnology University of Cambridge New Museums Site Pembroke Street Cambridge CB2 3RA CoMo United Kingdom GROUP Fax: + 44 (0)1223 334796 E-Mail:
[email protected] World Wide Web: http://como.cheng.cam.ac.uk/ Abstract This paper introduces a subdomain chemistry format for storing computa- tional chemistry data called CompChem. It has been developed based on the design, concepts and methodologies of Chemical Markup Language (CML) by adding computational chemistry semantics on top of the CML Schema. The format allows a wide range of ab initio quantum chemistry calculations of individual molecules to be stored. These calculations include, for exam- ple, single point energy calculation, molecular geometry optimization, and vibrational frequency analysis. The paper also describes the supporting in- frastructure, such as processing software, dictionaries, validation tools and database repositories. In addition, some of the challenges and difficulties in developing common computational chemistry dictionaries are discussed.