64 4 The Semantic Web and Bioinformatics Applications
Hypertext links are one of the most important features that the World
Wide Web adds to the underlying Internet. If one regards hypertext links
as defining relationships between resources, then the World Wide Web was
responsible for adding relationships to the resources that were already avail-
able on the Internet prior to the introduction of the web. Indeed, the name
“World Wide Web” was chosen because its purpose was to link together the
resources of the Internet into an enormous web of knowledge. However, as
we discussed in section 1.6, for relationships to be meaningful, they must be
explicit. As stated by Wittgenstein in Proposition 3.3 of (Wittgenstein 1922)),
“Only the proposition has sense; only in the context of a proposition has a
name meaning.” Unfortunately, hypertext links by themselves do not con-
vey any meaning. They do not explicitly specify the relationship between the
two resources that are linked.
The Semantic Web is a layer above the World Wide Web that adds meaning
to hypertext links. In other words, the Semantic Web makes hypertext links
into ontological relationships. The Semantic Web is a means for introducing
formal semantics to the World Wide Web. All reasoning in the Semantic Web
is formal and rigorous. The Semantic Web is defined by a series of progres-
sively more expressive languages and recommendations of the World Wide
Web Consortium. The first of these is the Resource Description Framework
(RDF) (Lassila and Swick 1999) which is introduced in this section. RDF is
developing quickly (Decker et al. 1998), and there are now many tools and
products that can process RDF. In section 4.4 we introduce the Web Ontology
Language (OWL) which adds many new semantic features to RDF.
As the name suggests, RDF is a language for representing information
about resources in the World Wide Web. It is particularly intended for repre-
senting annotations about web resources, such as the title, author, and mod-
ification date of a webpage. However, RDF can also be used to represent
information about anything that can be identified on the web, even when
it cannot be directly retrieved. Thus one could use URIs to represent dis-
eases, genes, universities, and hospitals, even though none of these are web
resources in the original sense.
The following is the beginning and end of the GO database, as expressed
in RDF:<go:go
xmlns:go="http://www.geneontology.org/dtds/go.dtd#"
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:RDF>
<go:term rdf:about="http://www.geneontology.org/go#GO:0003673"