Affiliations: Jena University Language and Information Engineering (JULIE) Lab, Jena, Germany | Institute of Medical Biometry and Medical Informatics, University Medical Center Freiburg, Freiburg, Germany | Institute for Formal Ontology and Medical Information Science (IFOMIS), Saarbrücken, Germany
Note:  Corresponding author.
Abstract: In the life sciences, there is an ample need for semantic interoperability of data. Thus shared vocabularies are needed for consistently expressing metadata in terms of semantic annotations as well as for querying bibliographic information systems. In the past years, lots of highly specialized, yet also fragmented terminologies have evolved. However, they lack principled forms of conceptual interlinkage. In order to provide an ontological basis for a seamless integration of such isolated parts of biological knowledge, we here introduce BioTop, an upper domain ontology for molecular biology. We describe its structure and contents, as well as its current interfaces to a selected set of OBO ontologies, which contain more detailed terminological knowledge about specific areas of molecular biology, e.g., cell types, molecular functions, biological processes and chemical compounds.