"The flood of data and factual knowledge in biology and medicine requires principled approaches to their proper analysis and management. A cornerstone in this effort constitutes the precise and complete description of the fundamental entities within this domain in terms of formal ontologies.
However, biomedical ontology development often still do not adhere to basic design principles: For example, even very low-level domain terms often lack precise and unambiguous (logical) definitions. This impedes the move towards semantic standardization that is needed for their intended knowledge management task. Rather, it leads to inconsistencies, fragmentation and overlap both within and inbetween different ontologies.
In light of this we introduce BioTop, a top-domain ontology that provides definitions for the foundational entities of biomedicine as a basic vocabulary to unambiguously describe facts in this domain. BioTop can furthermore serve as top-level model for creating new ontologies for more specific domains or as aid for aligning or improving existing ones.
BioTop is founded upon formal design principles (as propagated by the OBO Foundry initiative) and implemented in OWL-DL, the standard ontology language on the Semantic Web. BioTop makes use of the whole range of constructors of OWL-DL. The use of OWL-DL makes it possible to apply description logics reasoners for maintaining consistency by continuous classficiation during development and to automatically infer its hierarchical structure. To this end, we try to fully define as much classes as possible (in terms of necessary and sufficient conditions)."