Archive for the ‘CompChem’ Category

The Semantics of Chemical Markup Language (CML) for Computational Chemistry : CompChem

Sunday, August 12th, 2012

The Semantics of Chemical Markup Language (CML) for Computational Chemistry : CompChem by Weerapong Phadungsukanan, Markus Kraft, Joe A Townsend and Peter Murray-Rust (Journal of Cheminformatics 2012, 4:15 doi:10.1186/1758-2946-4-15)

Abstract (provisional):

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 (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 example, single point energy calculation, molecular geometry optimization, and vibrational frequency analysis. The paper also describes the supporting infrastructure, such as processing software, dictionaries, validation tools and database repository. In addition, some of the challenges and difficulties in developing common computational chemistry dictionaries are being discussed. The uses of CompChem are illustrated on two practical applications.

Important contribution if you are working with computational chemistry semantics.

Also important for its demonstration of the value of dictionaries and not trying to be all inclusive.

Integrate the data you have at hand and make allowance for the yet to be known.

Besides, there is always the next topic map that may consume the first with new merging rules.

CompChem Convention http://www.xml-cml.org/convention/compchem

CompChem dictionary http://www.xml-cml.org/dictionary/compchem/

CompChem validation stylesheet https://bitbucket.org/wwmm/cml-specs

CMLValidator http://bitbucket.org/cml/cmllite-validator-code

Chemical Markup Language (CML) http://www.xml-cml.org