The ontology of biological sequences.

Robert Hoehndorf, Janet Kelso, Heinrich Herre

Research output: Contribution to journalArticlepeer-review

18 Citations (SciVal)
135 Downloads (Pure)


BACKGROUND: Biological sequences play a major role in molecular and computational biology. They are studied as information-bearing entities that make up DNA, RNA or proteins. The Sequence Ontology, which is part of the OBO Foundry, contains descriptions and definitions of sequences and their properties. Yet the most basic question about sequences remains unanswered: what kind of entity is a biological sequence? An answer to this question benefits formal ontologies that use the notion of biological sequences and analyses in computational biology alike.

RESULTS: 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.

CONCLUSION: 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.
Original languageEnglish
Article number377
JournalBMC Bioinformatics
Publication statusPublished - 18 Nov 2009


Dive into the research topics of 'The ontology of biological sequences.'. Together they form a unique fingerprint.
  • A Formal Ontology of Sequences

    Hoehndorf, R., Kelso, J. & Herre, H., 01 Jul 2009, Proceedings of the First International Conference on Biomedical Ontologies (ICBO). Springer Nature

    Research output: Chapter in Book/Report/Conference proceedingConference Proceeding (Non-Journal item)

Cite this