Related Experiment Video
Updated: Jun 18, 2026

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
Published on: August 14, 2018
The ontology of biological sequences
Robert Hoehndorf1, Janet Kelso, Heinrich Herre
1Research Group Ontologies in Medicine, Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Haertelstrasse 16-18, 04107 Leipzig, Germany. leechuck@leechuck.de
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.
Related Concept Videos
Evolutionary Relationships through Genome Comparisons
Sequences
Genomics
Maxam-Gilbert Sequencing
Challenges of the Maxam-Gilbert Method
The...
Phylogenetic Trees
Multi-species Conserved Sequences
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved DNA...

