In philosophy, the term ontology has been used since the 17th century to refer both to a philosophical discipline (Ontology with a capital “O”), and as a domain-independent system of categories that can be used in the conceptualization of domain-specific scientific theories. In the past decades there has been a growing interest in the subject of ontology in computer and information sciences. In the last few years, this interest has expanded considerably in the context of the Semantic Web and MDA (Model-Driven Architecture) research efforts, and due to the role ontologies are perceived to play in these initiatives. In this paper, we explore the relations between Ontology and ontologies in the philosophical sense with domain ontologies in computer science. Moreover, we elaborate on formal characterizations for the notions of ontology, conceptualization and metamodel, as well as on the relations between these notions. Additionally, we discuss a set of criteria that a modeling language should meet in order to be considered a suitable language to model phenomena in a given domain, and present a systematic framework for language evaluation and design. Furthermore, we argue for the importance of ontology in both philosophical senses aforementioned for designing and evaluating a suitable general ontology representation language, and we address the question whether the so-called Ontology Web languages can be considered as suitable general ontology representation languages. Finally, we motivate the need for two complementary classes of modeling languages in Ontology Engineering addressing two separate sets of concerns.