Modelling Molecular Biological Information: Ontologies and Ontological Design Patterns

Abstract

The amount of available information in molecular biology is vast due to genome sequencing and gene expression chips. Nowadays, the challenge is to represent and manage the static and dynamic properties of DNA sequence data or annotated information to decipher the structural, functional and evolutionary clues encoded in biological sequences. Therefore, molecular biologists build and use ontologies to represent parts of the molecular biological terminology and to provide a model of biological concepts. Ontological Design Patterns (ODPs) provide a technique to increase the flexibility and reusability of these biological ontologies. There are many useful features of ODPs: 1) they describe simple, flexible and reusable solutions to specific design problems, 2) they can be defined and applied within informal or formal ontologies, 3) they make design approaches transferable, clarify the architecture, and improve the documentation of ontology-based knowledge systems, and 4) they form a framework to deal with different bio-informatics tasks, such as accessing and managing heterogeneous molecular biological databases, analysing scientific texts, or annotating sequence databases. Most of the ODPs are informally described in (Reich, 1999). All ODPs with code examples are available from the author.