4

The Semantic Web and

Bioinformatics Applications

Many people have had the experience of suddenly realizing that two of their

acquaintances are actually the same person, although it usually is not as dra-

matic as it was for the main characters in the movieYou’ve Got Mail.The

other kind of identity confusion is considerably more sinister: two persons

having the same identity. This is a serious problem, known asidentify theft.

The issue of whether two entities are the same or different is fundamental to

semantics.

Addressing logical issues such as whether two entities are the same re-

quires substantially more powerful reasoning capabilities than XML DTDs

or schemas provide. Someday, automated reasoners and expert systems may

be ubiquitous on the web, but at the moment they are uncommon. The web

is a powerful medium, but it does not yet have any mechanism for rules

and inference. Tim Berners-Lee, the director of the World Wide Web Consor-

tium, has proposed a new layer above the web which would make all of this

possible. He calls this theSemantic Web(Miller et al. 2001).

The World Wide Web is defined by a language, the Hypertext Markup Lan-

guage (HTML), and an Internet protocol for using the language, the Hyper-

text Transfer Protocol (HTTP). In the same way, the Semantic Web is defined

by languages and protocols. In this chapter, we introduce the languages of

the Semantic Web and explain what they mean.

4.1 The Semantic Web in Bioinformatics

Biologists use the web heavily, but the web is geared much more toward hu-

man interaction than automated processing. While the web gives biologists

access to information, it does not allow users to easily integrate different

data sources or to incorporate additional analysis tools. The Semantic Web