Computational Chemistry Data Management Platform Based on the Semantic Web

Bing Wang; Paul A Dobosh; Stuart Chalk; Mirek Sopek; Neil S Ostlund

doi:10.1021/acs.jpca.6b10489

Computational Chemistry Data Management Platform Based on the Semantic Web

J Phys Chem A. 2017 Jan 12;121(1):298-307. doi: 10.1021/acs.jpca.6b10489. Epub 2016 Dec 22.

Authors

Bing Wang¹, Paul A Dobosh¹, Stuart Chalk², Mirek Sopek¹, Neil S Ostlund¹

Affiliations

¹ Chemical Semantics Inc. , 2772 NW 43rd Street, Suite B1, Gainesville, Florida 32606, United States.
² Department of Chemistry, University of North Florida , Jacksonville, Florida 32224, United States.

PMID: 27936706
DOI: 10.1021/acs.jpca.6b10489

Abstract

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.