Over the past few months I have been working on how to represent biological taxonomy and nomenclature using Description Logics. Here I combine these thoughts with a rather naive view of DNA Barcoding to suggest a new approach to taxonomy.
Description Logic (DL) is an extension of frame based languages (such as those used in object orientated programming paradigms) and semantic networks (e.g. WordNet) to link them to first-order predicate logic thus enabling the representation of application domains in formal, well understood ways that can be reasoned over by machines. DL has come to the fore in recent years with the advent of the Web Ontology Lanugage (OWL) by the World Wide Web Consortium (W3C). Two subsets of which, OWL-DL and OWL-Lite, are based on DL. Notably these two sub-languages guarantee decidability within finite time. From now on I’ll use the terminology of OWL-DL and OWL-Lite rather than generic DL terms. The OWL terms are more likely to be understood by a general reader who can read the OWL documentation as background. A concept in DL is referred to as a class in OWL. A role in DL is a property in OWL.
There are three principal features within OWL:
- Classes are groups of individuals that belong together typically because they share some properties or property values.
- Individuals are instances of classes.
- Properties are statements of relationships between individuals or from individuals to data values.
There are other features within the language that allow the expression of things such as equivalence, cardinality and the domains and ranges of properties. Using OWL principally involves asserting specialization hierarchies of classes and inferring unknown subclass relationships and class membership using an inference engine such as Fact++. A set of OWL assertions is frequently referred to as an ontology.