The Ontology for Molecular Biology

The Ontology for Molecular Biology (MBO) is an attempt to provide clarity and communication within the molecular biology database community [2]. The use of MBO would avoid `semantic confusion', such as that which arises with the use of the concept of Gene (see Section 1). Schulze-Kremer claims `By adhering to a commonly agreeable ontology, uncertainty and misunderstanding about the semantic relations between database entries from different databases can be eliminated.' This would mean that either the different databases agreed to the common MBO definition (and changed their annotations accordingly) or inferences about the differences between each databases conceptualisation of `gene' could be made in terms of the MBO. In either case, attempts could then be made to reconcile or interoperate between the databases.

The MBO contains concepts and relationships that are required to describe biological objects, experimental procedures and computational aspects of molecular biology [2]. It is very wide ranging and has over 1200 nodes representing both concepts and instances. In the conceptual part of the MBO, the primary relationship used is the `is a kind of' relationship. The MBO has an organising, upper-level ontology. The root concept ``Being' divides into `object' and `event'. `Object', for instance, is subdivided into `physical-' and `abstract-' object. This helps give a precise classification for lower level concepts - so, `physics objectis an `abstract object' and `DNA' a `physical-object'. MBO defines a linkage map from GDB in the following way: `DBObject$\cdot$MappingObject$\cdot$Map$\cdot$LinkageMap' (the $\cdot$ represents the sub-concept relationship).

The actual biological content of the MBO is currently relatively small, ending at quite large grained concepts such as Protein, Gene, and Chromosome. The framework, however, exists for extending the MBO much further into the biological domain.