The PROTON Ontology (PROTo ONtology) is a basic upper-level ontology that contains about 300 classes and 100 properties, providing coverage of the general concepts necessary for a wide range of tasks, including semantic annotation, indexing, and retrieval of documents.

The proton is a subatomic particle, symbol or , with a positive electric charge of +1e elementary charge and mass slightly less than that of a neutron. Protons and neutrons, each with mass approximately one atomic mass unit, are collectively referred to as "nucleons". One or more protons are present in the nucleus of every atom. The number of protons in the nucleus is the defining property of an element, and is referred to as the atomic number. Since each element has a unique number of protons, each element has its own unique atomic number. The word proton is Greek for "first", and this name was given to the hydrogen nucleus by Ernest Rutherford in 1920. In previous years Rutherford had discovered that the hydrogen nucleus (known to be the lightest nucleus) could be extracted from the nuclei of nitrogen by collision. The proton was therefore a candidate to be a fundamental particle and a building block of nitrogen and all other heavier atomic nuclei.