Definition: An entity feature that represents the covalently modified state of a dna, rna or a protein. Rationale: In Biology, identity of DNA, RNA and Protein entities are defined around a wildtype sequence. Covalent modifications to this basal sequence are represented using modificaton features. Since small molecules are identified based on their chemical structure, not sequence, a covalent modification to a small molecule would result in a different molecule. Usage: The added groups should be simple and stateless, such as phosphate or methyl groups and are captured by the modificationType controlled vocabulary. In other cases, such as covalently linked proteins, use CovalentBindingFeature instead. Instances: A phosphorylation on a protein, a methylation on a DNA.
Source:http://www.biopax.org/release/biopax-level3.owl#ModificationFeature