Why does BioPAX have a simple ontology using a limited number of classes instead of creating many specialized classes?
• Early on, it was decided that BioPAX would not try to create many specialized classes for the following reasons: • It is difficult for a group of people to agree on how to classify things as you get into more specific classes, but it is usually relatively easy to get agreement on a general classification scheme. For instance, should small molecules be specialized to aromatic and aliphatic compounds or should they be specialized into alcohols, phenols, carboxylates, etc. Few people would disagree with the need to represent small molecules in BioPAX, but many would disagree with any one subclassification. • Fewer classes makes BioPAX more general for a wider number of users. For instance, the inclusion of eukaryotic cellular locations directly in BioPAX makes BioPAX more difficult to use for those only interested in prokaryotic biology. On the other hand, if a simple cellular location class is used for all cellular locations (and another ontology is referenced to describe them), then i
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