ModelingApproach

Modeling approach

Some of this was previously entered under classes vs instances

The anatomy ontology at the moment is a slightly confusing mixture of classes and instances. I think to clear this up we need to draw some clear lines about what the classes are representing and what the instances are representing.

The classes we create and the properties defined on them form a meta model for the instances. The definition of classes and properties is a meta-meta model. Therefore, the classes we define should hold information about the properties we need to fill out and the associations between instances that can be made. In our case, we should not be using these classes to define actual biological types, in the end, they just end up being classes with the same kinds of properties but different labels. If we were building a defined ontology using say OWL, then we could define some biological types that are defined on the basis of their property restrictions. But we are not doing this. A very good example of that kind of ontology is the TAMBIS ontology(for the ontology in OWL form see TAMBISOWLONTOLOGY). Our ontology instead should just define the top level classes that it does, like Anatomical Type and not hierarchies of actual biological forms like Blood vessel.

The proposal would be to add some properties to AnatomicalType, or specialize AnatomicalType to provide properties such as part_of, or types such as anatomical_compartment.

Another value we get from using instances to hold all our content rather than a mixture of classes and instances is so we can operate better across other ontologies and databases. If we bind too much information up in our Class descriptions, then we may be making these inaccessible to other modeling environments. If instead we bundle all the useful property values into an instance, then we can at least port those frames into other database forms, or test whether they conform to alternative models.

This message is an interesting point in a thread the use of OWL classes as instances. In this case, the person wanted to use an OWL class as the subject of 'dc:Subject' from the dublin core specification. Watch for the split in the thread, so make sure you follow this part too.