Computational Chemistry Data Management Platform Based on the Semantic Web

• Published in: The journal of physical chemistry. A, Molecules, spectroscopy, kinetics, environment, & general theory Vol. 121; no. 1; pp. 298 - 307
• Main Authors: Wang, Bing, Dobosh, Paul A, Chalk, Stuart, Sopek, Mirek, Ostlund, Neil S
• Format: Journal Article
• Language: English
• Published: United States American Chemical Society 12.01.2017
• Subjects: Chemistry; Physics
• ISSN: 1089-5639; 1520-5215; 1520-5215
• DOI: 10.1021/acs.jpca.6b10489

This paper presents a formal data publishing platform for computational chemistry using semantic web technologies. This platform encapsulates computational chemistry data from a variety of packages in an Extensible Markup Language (XML) file called CSX (Common Standard for eXchange). On the basis of a Gainesville Core (GC) ontology for computational chemistry, a CSX XML file is converted into the JavaScript Object Notation for Linked Data (JSON-LD) format using an XML Stylesheet Language Transformation (XSLT) file. Ultimately the JSON-LD file is converted to subject–predicate–object triples in a Turtle (TTL) file and published on the web portal. By leveraging semantic web technologies, we are able to place computational chemistry data onto web portals as a component of a Giant Global Graph (GGG) such that computer agents, as well as individual chemists, can access the data.