304 12 Building Bioinformatics Ontologies
muscles, organs, skin, and so on. While one can have an ontology consisting
of just a class hierarchy, such as the many classic taxonomies, they are just as
lifeless as a skeleton by itself. Properties are essential for giving an ontology
real meaning.
Properties can be classified in several ways:- Attribute vs. relationship. In XML, attributes are very different from
child elements, both syntactically and semantically, as discussed in sec-
tion 2.2. RDF and OWL eliminate this distinction, as explained in sec-
tion 4.2. - Data vs. resource.XSD is in two parts. The first part deals with data struc-
tures (made up of XML elements) and the second deals with datatypes
(such as numbers and dates, which do not involve XML elements). In
XML, data structures are built using child elements. For example, a Med-
line citation such as figure 2.1 is an elaborate data structure using many
elements. A simple datatype value, on the other hand, can be represented
in XML using either XML attributes or XML elements. For example, the
fact that George’s height is 185 can be expressed either as an attribute:
<Person name="George" height="185"/>or as a child element:<Person name="George">
<height>185</height>
</Person>- Intrinsic or extrinsic. A property isintrinsicif it is a fundamental fea-
ture of the entity. For example, the chemical formula and structure of
an enzyme is intrinsic. Properties that are not intrinsic are said to beex-
trinsic. For example, the name of an enzyme is extrinsic. To tell whether a
property is intrinsic or extrinsic ask whether changing the property would
change the entity. Changing the name of an enzyme would not normally
be regarded as changing it in a fundamental way. Changing its chemical
formula, however, would normally be seen as changing the enzyme.
Although being intrinsic or extrinsic is an important feature of a prop-
erty, none of the major ontology languages have such a notion. At the