74 4 The Semantic Web and Bioinformatics Applications
- Range rule.If propertyPhasrangeC, and if the resourceRis linked to
resourceSusing propertyP, then the resourceRhasrdf:typeC.
The full list of all RDF inference rules is in (Hayes 2004).
The meaning of an RDF graph is intimately connected with the RDF rules.
Any query or other use of an RDF graph always presumes that all applicable
inference rules have been applied. This is very different from XML where
“what you see is what you get,” that is, the meaning of XML is entirely de-
termined by what is explicitly stated. Rules can be a powerful mechanism
for expressing meaning, but this power comes at a price. The subClass rule,
for example, is very powerful and useful, but because it does not allow for
the possibility of any exceptions, it is not applicable to many taxonomies in
the real world. As another example, suppose one makes a mistake and states
that a Medline citation is owned by rhodopsin. This does not make sense:
rhodopsin is a protein not an institution. An XML processor would imme-
diately give an error message, but an RDF processor would not. The RDF
processor would just infer that rhodopsin is both a protein and an institution!
One flaw of XML is that the order of child elements is semantically signifi-
cant whether one wants it to be significant or not. RDF allows one to choose
whether the order should matter or not, and it provides two mechanisms
for this. The older mechanism is the notion of acontainer. For example, the
Krebs cycle is an ordered list of eight enzymes.^1 Using ordinary XML, order
matters, so one could define the Krebs cycle enzymes with the following:<Pathway name="Krebs Cycle">
<Protein name="Citrate synthase"/>
<Protein name="Aconitase"/>
<Protein name="Isocitrate dehydrogenase"/>
<Protein name="a-Ketoglutarate dehydrogenase complex"/>
<Protein name="Succinyl-CoA synthetase"/>
<Protein name="Succinate dehydrogenase"/>
<Protein name="Fumerase"/>
<Protein name="Malate dehydrogenase"/>
</Pathway>In RDF the relationship must be explicitly specified so it would look some-
thing like this:- It is actually a cycle. The order is significant, but one can start with any one of the enzymes.