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The ontology of biological sequences

DOI: 10.1186/1471-2105-10-377

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Abstract:

We provide both an ontological analysis of biological sequences and a formal representation that can be used in knowledge-based applications and other ontologies. We distinguish three distinct kinds of entities that can be referred to as "biological sequence": chains of molecules, syntactic representations such as those in biological databases, and the abstract information-bearing entities. For use in knowledge-based applications and inclusion in biomedical ontologies, we implemented the developed axiom system for use in automated theorem proving.Axioms are necessary to achieve the main goal of ontologies: to formally specify the meaning of terms used within a domain. The axiom system for the ontology of biological sequences is the first elaborate axiom system for an OBO Foundry ontology and can serve as starting point for the development of more formal ontologies and ultimately of knowledge-based applications.Biological sequences play a major role in genetics and bioinformatics research. They are important in the description of DNA, RNA and proteins, and are among the basic entities studied in molecular and computational biology. In the realm of biological ontologies, the Sequence Ontology (SO) [1] was developed to describe sequences and their features semantically. Although many formal definitions are available for the SO categories, several categories remain defined using natural language.Formal ontologies are intended to formally specify a conceptualization of a domain [2], and therefore provide the foundation for data and information integration and exchange. Definitions alone are insufficient to achieve this goal. Axioms are required to provide meaning for primitive, undefined categories and relations. To provide an ontological analysis of "biological sequence" and to formalize the basic categories used in the SO, several ontological questions about sequences must be answered, among them: what kind of entity is a biological sequence? How does it relate to spac

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