As the biomedical domain is highly interconnected, bio-ontologies may overlap with each other. For instance, the Ontology of Biomedical Investigation (OBI) requires the availability of definitions for those chemicals used in any investigation. These definitions do not need to be developed within the OBI ontology as there is already a biomedical ontology for the domain of chemicals, called ChEBI. Similarly, software, such as Array Express, making use of an ontology may require more than a single domain ontology. Typically, in these types of scenarios, it is necessary to integrate multiple ontologies into a single coherent narrative. In order to integrate or re-use specific domain ontologies following this “building-block” approach there has to be a high level structure or common “scaffold” where different parts of different domain ontologies may be “plugged” into. To ensure ease of interoperation, or re-use of a domain ontology, well designed and documented ontologies, are essential, and upper ontologies are fundamental in this integrative effort.
Upper level ontologies provide a domain independent conceptual model that aims to be highly re-usable across specific domain applications. One of the primary purposes of upper ontologies is to aid semantic integration across ontologies and to encourage a set of design principles within those ontologies that use them. Upper ontologies usually describe very general level or abstract concepts. Most of the upper ontologies provide a general classification criterion that makes it easy to re-use, extend and maintain those existing ontologies required by a particular application. Therefore, it is essential, to aid interoperability and re-use, that ontology development methodologies should provide general guidelines for the use of upper level ontologies. These guidelines should cover the documentation of
Examples of upper level ontologies include: the Basic Formal Ontology (BFO), DOLCE and GFO. Depending on an upper ontologies representation, or “world view” the upper ontology will provide a framework on how to model, physical objects, processes and information and provide contraints on how these classes are related to each other.