Information on Chemistry Ontologies
Table of Contents
OntoSpecies
OntoSpecies serves as core ontology within TWA chemistry domain. It is an ontology for the semantic representation of chemical species and their properties. It covers a diverse collection of identifiers, classifications and uses of chemical species, as well as spectral data. The data on chemical species is sourced from PubChem and ChEBI.
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Access
- Direct access via Blazegraph Workbench (select "ontospecies" namespace)
- SPARQL endpoint: https://theworldavatar.io/chemistry/blazegraph/namespace/ontospecies
Publications
[1] F. Farazi, N. Krdzavac, J. Akroyd, S. Mosbach, A. Menon, D. Nurkowski, and M. Kraft, "Linking reaction mechanisms and quantum chemistry: An ontological approach", Computers & Chemical Engineering, 137, 106813, (2020)
[2] L. Pascazio, S. D. Rihm, A. Naseri, S. Mosbach, J. Akroyd, and M. Kraft, "A chemical species ontology for data integration and knowledge discovery", Journal of Chemical Information and Modeling, (2023)
[3] L. Pascazio, D. Tran, S. D. Rihm, Jiaru Bai, J. Akroyd, S. Mosbach, and M. Kraft, "Question-answering system for combustion kinetics", Proceedings of the Combustion Institute, 40, 105428, (2024)
Preprints
[1] F. Farazi, N. Krdzavac, J. Akroyd, S. Mosbach, A. Menon, D. Nurkowski, and M. Kraft, "Linking reaction mechanisms and quantum chemistry: An ontological approach", Technical Report 236, c4e-Preprint Series, Cambridge, 2019 (PDF)
[2] L. Pascazio, S. D. Rihm, A. Naseri, S. Mosbach, J. Akroyd, and M. Kraft, "A chemical species ontology for data integration and knowledge discovery", Technical Report 306, c4e-Preprint Series, Cambridge, 2023 (PDF)
[3] L. Pascazio, D. Tran, S. D. Rihm, Jiaru Bai, J. Akroyd, S. Mosbach, and M. Kraft, "Question-answering system for combustion kinetics", Technical Report 315, c4e-Preprint Series, Cambridge, 2023 (PDF)
OntoKin
OntoKin is an ontology designed to represent reaction mechanisms. It details sets of stoichiometric reactions that define reaction mechanisms, characterizing each reaction through its reactants and products. These components are further described by their thermodynamic properties and transport behaviors. OntoKin supports various reaction types, including gas-phase and surface reactions, utilizing several kinetic models to accommodate different scenarios. This ontology facilitates the integration and comparison of kinetic, thermodynamic, and transport data across the literature.
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Access
- Direct access via Blazegraph Workbench (select "ontokin" namespace)
- SPARQL endpoint: https://theworldavatar.io/chemistry/blazegraph/namespace/ontokin
Publications
[1] F. Farazi, J. Akroyd, S. Mosbach, P. Buerger, D. Nurkowski, M. Salamanca, and M. Kraft, "OntoKin: An ontology for chemical kinetic reaction mechanisms", Journal of Chemical Information and Modeling, 60, 1, 108-120, (2020)
[2] F. Farazi, N. Krdzavac, J. Akroyd, S. Mosbach, A. Menon, D. Nurkowski, and M. Kraft, "Linking reaction mechanisms and quantum chemistry: An ontological approach", Computers & Chemical Engineering, 137, 106813, (2020)
[3] L. Pascazio, D. Tran, S. D. Rihm, Jiaru Bai, J. Akroyd, S. Mosbach, and M. Kraft, "Question-answering system for combustion kinetics", Proceedings of the Combustion Institute, 40, 105428, (2024)
Preprints
[1] F. Farazi, J. Akroyd, S. Mosbach, P. Buerger, D. Nurkowski, and M. Kraft, "OntoKin: An ontology for chemical kinetic reaction mechanisms", Technical Report 218, c4e-Preprint Series, Cambridge, 2019 (PDF)
[2] F. Farazi, N. Krdzavac, J. Akroyd, S. Mosbach, A. Menon, D. Nurkowski, and M. Kraft, "Linking reaction mechanisms and quantum chemistry: An ontological approach", Technical Report 236, c4e-Preprint Series, Cambridge, 2019 (PDF)
[3] L. Pascazio, D. Tran, S. D. Rihm, Jiaru Bai, J. Akroyd, S. Mosbach, and M. Kraft, "Question-answering system for combustion kinetics", Technical Report 315, c4e-Preprint Series, Cambridge, 2023 (PDF)
OntoCompChem
OntoCompChem is an ontology designed to represent the input and output processes of quantum mechanical (QM) calculations, with a primary focus on molecular systems. This ontology delineates calculations through various detailed parameters: the objective (e.g., single point calculation, geometry optimization, frequency calculation), the utilized software (e.g., Gaussian16), the theoretical level employed (e.g., B3LYP, 6-31G(d)), and additional details such as overall charge and spin polarization. Furthermore, OntoCompChem includes data on calculated frontier orbitals, the final converged self-consistent field (SCF) energy, optimized geometries for geometry optimizations, and for frequency calculations, it records the zero-point energy correction and a comprehensive list of computed vibrational frequencies, linking back to their corresponding stationary geometries and calculations.
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Access
- Direct access via Blazegraph Workbench (select "ontocompchem" namespace)
- SPARQL endpoint: https://theworldavatar.io/chemistry/blazegraph/namespace/ontocompchem
Publications
[1] N. Krdzavac, S. Mosbach, D. Nurkowski, P. Buerger, J. Akroyd, J. W. Martin, A. Menon, and M. Kraft, "An ontology and semantic web service for quantum chemistry calculations", Journal of Chemical Information and Modeling, 59(7), 3154-3165, (2019).
[2] F. Farazi, N. Krdzavac, J. Akroyd, S. Mosbach, A. Menon, D. Nurkowski, and M. Kraft, "Linking reaction mechanisms and quantum chemistry: An ontological approach", Computers & Chemical Engineering, 137, 106813, (2020).
[3] L. Pascazio, D. Tran, S. D. Rihm, Jiaru Bai, J. Akroyd, S. Mosbach, and M. Kraft, "Question-answering system for combustion kinetics", Proceedings of the Combustion Institute, 40, 105428, (2024).
Preprints
[1] N. Krdzavac, S. Mosbach, D. Nurkowski, P. Buerger, J. Akroyd, J. W. Martin, A. Menon, and M. Kraft, "An ontology and semantic web service for quantum chemistry calculations", Technical Report 223, c4e-Preprint Series, Cambridge, 2019 (PDF).
[2] F. Farazi, N. Krdzavac, J. Akroyd, S. Mosbach, A. Menon, D. Nurkowski, and M. Kraft, "Linking reaction mechanisms and quantum chemistry: An ontological approach", Technical Report 236, c4e-Preprint Series, Cambridge, 2019 (PDF).
[3] L. Pascazio, D. Tran, S. D. Rihm, Jiaru Bai, J. Akroyd, S. Mosbach, and M. Kraft, "Question-answering system for combustion kinetics", Technical Report 315, c4e-Preprint Series, Cambridge, 2023 (PDF).
OntoZeolite and OntoCrystal
OntoZeolite and OntoCrystal are semantically interconnected ontologies to represent information on zeolite materials and integrate it with information on zeolite topologies and their construction, crystalline information and information on non-framework chemical species functioning as guest or charge-balancing ions.
The OntoZeolite ontology provides a structured framework that contextualises zeolites-related knowledge. Its core concept - ZeoliteFramework - is used to instantiate information about individual framework types (e.g. FAU, LTA, NAT etc.) and connects to topological properties, synthesised zeolites, as well as crystal information.
The OntoCrystal ontology provides a semantic representation of crystallographic data. The central concept in the OntoCrystal ontology, CrystalInformation, is used to store fundamental crystallographic information and aggregates data from five key classes: UnitCell, XRDSpectrum, AtomicStructure, CoordinateTransformation, and TiledStructure.
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Access
- Direct access via Blazegraph Workbench (select "ontozeolite" namespace)
- SPARQL endpoint: https://theworldavatar.io/chemistry/blazegraph/namespace/ontozeolite
Preprints
[1] A. Kondinski, P. Rutkevych, L. Pascazio, D. Tran, F. Farazi, S. Ganguly, and M. Kraft, "Knowledge Graph Representation of Zeolitic Crystalline Materials", Technical Report 321, c4e-Preprint Series, Cambridge, 2024 (PDF).
OntoMOPs
The OntoMOPs ontology is designed to provide and enrich semantic relationships between metal-organic polyhedra (MOPs), their chemical building units (CBUs), and assembly models (AMs). OntoMOPs links MOP instances to metadata such as molecular mass, charge, formulae, and provenance information like DOIs and CCDC numbers.
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Publications
[1] A. Kondinski, A. Menon, D. Nurkowski, F. Farazi, S. Mosbach, J. Akroyd, and M. Kraft, "Automated Rational Design of Metal–Organic Polyhedra", Journal of the American Chemical Society, 144(26), 11713-11728, (2022).
Preprints
[1] A. Kondinski, A. Menon, D. Nurkowski, F. Farazi, S. Mosbach, J. Akroyd, and M. Kraft, "Automated Rational Design of Metal-Organic Polyhedra", Technical Report 292, c4e-Preprint Series, Cambridge, 2022 (PDF).
[2] D. Tran, S. D. Rihm, A. Kondniski, L. Pascazio, F. Saluz, S. Mosbach, J. Akroyd, and M. Kraft, "Natural Language Access Point to Digital Metal-Organic Polyhedra Chemistry in The World Avatar", Technical Report 327, c4e-Preprint Series, Cambridge, 2024 (PDF).