A conceptual basis to define and detect organic functional groups is developed. The basic model of a functional group is termed as a primary functional group and is characterized by a group center composed of one or more group center atoms bonded to terminal atoms and skeletal carbon atoms. The generic group center patterns are identified from the structures of known functional groups. Accordingly, a chemical ontology 'Font' is developed to organize the existing functional groups as well as the new ones to be defined by the chemists. The basic model is extended to accommodate various combinations of primary functional groups as functional group assemblies. A concept of skeletal group is proposed to define the characteristic groups composed of only carbon atoms to be regarded as equivalent to functional groups. The combination of primary functional groups with skeletal groups is categorized as skeletal group assembly. In order to make the model suitable for reaction modeling purpose, a Graphical User Interface (GUI) is developed to define the functional groups and to encode in XML format appropriate to detect them in chemical structures. The system is capable of detecting multiple instances of primary functional groups as well as the overlapping poly-functional groups as the respective assemblies.