OntoCompChem (ONTOCOMPCHEM)

2007, offering a user-friendly interface that allows researchers and practitioners to easily access and query information about chemical mechanisms. This QA system is a key component of “The World Avatar” (TWA), a dynamic framework built upon semantic web technologies. TWA is characterized by its layered structure, which includes a knowledge graph (KG), software agents, and real-world data integration. These layers collectively create a comprehensive unified system for managing and analyzing complex chemical data from various domains. We detail the enhancements made to TWA’s ontologies (OntoSpecies, OntoKin, and OntoCompChem) to meet specific challenges in chemical kinetics and improve their representation accuracy. By focusing on data provenance and interoperability, our approach ensures transparent and reliable data management that adheres to the FAIR principles, which is vital for precise information retrieval and analysis. The role of software agents in populating these ontologies is highlighted, showcasing how they transform raw data into meaningful structured knowledge and generate new insights within the TWA ecosystem. Additionally, the semantic web technologies’ interoperability feature facilitates data integration and exchange across different platforms and tools, making the data machine-actionable. We instantiated in the KG data on four H2/O2 and five CH4/O2 reaction mechanisms taken from the literature and we then demonstrate the QA system’s capabilities in answering questions related to these reaction mechanisms as a proof of concept. Lastly, we discuss the future directions of the TWA framework, which include not only future extensions of the QA system but also the integration of external tool to automate tasks such as generation of kinetic mechanism, further expanding TWA’s functionality and application in the field of chemical kinetics.

The World Avatar (TWA) project. OntoPESScan is linked to other ontologies for chemistry in TWA, including OntoSpecies, which helps uniquely identify species along the PES and access their properties, and OntoCompChem, which allows the association of potential energy surfaces with quantum chemical calculations and the concepts used to derive them. A force-field fitting agent is also developed that makes use of the information in the OntoPESScan ontology to fit force fields to reactive surfaces of interest on the fly by making use of the empirical valence bond methodology. This agent is demonstrated to successfully parametrize two cases, namely, a PES scan on ethanol and a PES scan on a localized π-radical PAH hypothesized to play a role in soot formation during combustion. OntoPESScan is an extension to the capabilities of TWA and, in conjunction with potential further ontological support for molecular dynamics and reactions, will further progress toward an open, continuous, and self-growing knowledge graph for chemistry.

based on the semantics of concepts specified in the CompChem convention of Chemical Markup Language (CML) and by extending the Gainesville Core (GNVC) ontology. MolHub is developed in order to establish semantic interoperability between different tools used in quantum chemistry and thermochemistry calculations, and as such is integrated into the J-Park Simulator (JPS)—a multidomain interactive simulation platform and expert system. It uses the OntoCompChem ontology and implements a formal language based on propositional logic as a part of its query engine, which verifies satisfiability through reasoning. This paper also presents a NASA polynomial use-case scenario to demonstrate semantic interoperability between Gaussian and a tool for thermodynamic data calculations within MolHub.