Chemical Semantics, Inc. is a company with a mission of bringing the semantic web to computational chemistry, with future goals covering chemical results from other areas. The company has built a universal portal that enables computational chemists to publish results of their computations on semantic web servers (powered by semantic triple stores) holding RDF data. This presentation will report the work of the definition, implementation and evaluation of a new data model based on semantic web standards. This new model exploits further the RDF data model for efficient encoding of the molecular structures and basic results of computational chemistry experiments. Various serializations methods were tested including Turtle and JSON-LD. The model is exceptionally flexible and allows for various types of chemical structure representation (e.g. Cartesian, fractional or based on Z-matrix). It enables the encoding of various structural units like residues for polymers and biopolymers and groups. Efficient encoding of bonding information enables fast substructure searches using standard tools like SPARQL and application in the domain of cheminformatics. The model offers maximum possible flexibility, allowing users to add their own data without the destroying the readability of the core elements. The model enables practitioners to interact with the data in much more flexible way using variety of current programming tools and languages. The most important aspect of the model is its fully semantic character, i.e. encoding the meaning of the data in the data itself through the reference to the new edition of Gainesville Core ontology1. [1] Neil Ostlund, Mirek Sopek, Proceedings of the 6th International Workshop on Semantic Web Applications and Tools for Life Sciences, Edinburgh, UK, December 10, 2013. http://ceur-ws.org/Vol-1114

Representation of molecular structures and related computations on the semantic web: A universal data model and its ontology

251st National Meeting (2016)

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