84 4 The Semantic Web and Bioinformatics Applications
<owl:Class rdf:ID="Gene">
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="#occursIn"/>
<owl:someValuesFrom rdf:resource="#Species"/>
</owl:Restriction>
</rdfs:subClassOf>
</owl:Class>Now suppose that we state that hemoglobin alpha embryonic-3 (hbae3)isa
gene but neglect to mention any species that this gene occurs in:<Gene rdf:ID="hbae3">
<rdfs:label>hemoglobin alpha embryonic-3</rdfs:label>
</Gene>If we are assuming a closed world, then this annotation is inconsistent: one is
required to specify at least one species in which each gene occurs. In an open
world, on the other hand, one can infer that this gene occurs in some species,
we just do not know which ones they are. In an open world, one accepts that
one does not know everything, and that some facts have yet to be stated. In
a closed world, the world is assumed to be “complete”: if something has not
been stated then it is not true.
The closed world assumption has been used successfully for many years
by database management systems, and there are good reasons for making
this assumption. Databases arose in the context of commercial business ap-
plications. For example, they are used for storing employee information. If
a person does not have a record in the employee database, then the person
is not an employee. This may seem unduly harsh, but it makes perfectly
good sense for modern businesses where all significant records are stored in
databases. Modern storage systems can be made highly reliable and fault tol-
erant, so much so that they are now more reliable than paper documents. In
this case, the database is not simply recording the state of reality, itisreality.
Being an employee isdefinedby records stored in the computer system.
By contrast, the closed world assumption is not appropriate for the web
where information is necessarily incomplete and fragmentary. The web con-
sists of a very large number of independent websites for which there is no
central authority. Furthermore, websites can be turned on and off at the
whim of the owners.