OCE: The Ontology of Chemical Elements
The year of 2019 marked the 150th anniversary of the Mendeleev’s invention of the Periodic Table of Chemical Elements. Although the Periodic Table has many advantages, it also has shortcomings including the lack of machine readability and computer-assisted reasoning. Ontology has been emerging to play significant roles in data and knowledge standardization, integration, sharing, reasoning, and analysis. In our 2019 study, we demonstrated that ontology can be used to precisely derive Mendeleev’s Periodic Table, and we could also extend the strategy of precise ontology definition and representation to derive the modern version of the Periodic Table of Chemical Elements.
The basic information of chemical elements has been represented in the Chemical Entities of Biological Interest (ChEBI), a database and ontology of chemical entities related to biological studies (https://www.ebi.ac.uk/chebi/). The ChEBI ontology stores and represents about 15,000 chemical entities and regroups them based on common structural characteristics. For each chemical element, ChEBI includes different annotations such as name, text definition, hierarchy, mass, and biological roles. However, ChEBI does not provide some important features of the known 118 chemical elements, such as group and period (which are key to the periodic table), electronegativity, and valence shell structure. Some important annotation information is also not available in ChEBI.
To systematically represent and study chemical elements, we have then generated the community-driven Ontology of Chemical Elements (OCE). OCE only focuses on the known 118 chemical elements and their charactistics and relations with other entities. The OCE ontology is primarily developed by Dr. Kaiyong Liu from Anhui Medical University, Hefei, Anhui, China, and Yongqun "Oliver" He from University of Michigan Medical School, Ann Arbor, MI, USA.
Kaiyong Liu, Yongqun He. Ontological Derivation of Mendeleev’s Periodic Table of Chemical Elements. The 10th International Conference on Biomedical Ontology (ICBO-2019), July 30 - August 2, 2019, Buffalo, NY, USA. One-page short article. Poster presentation.
https://raw.githubusercontent.com/ontologyofchemicalelements/OCE/master/src/oce-merged.owl
BioPortal: https://bioportal.bioontology.org/ontologies/success/OCE