An Exemplatory Ontology

This ontology is developed to facilitate the discussion for our manuscript From XML to RDF - How semantic web technologies will change the design of 'omic' standards published at Nature Biotechnology, 23 (2005) 1099-1103.. This ontology defines detailed usage of an examplatory ontology. The ontology is created for demonstrative purpose of a prepared manuscript. The ontology is therefore not intended to be complete. If you are interested to use a suitable ontology to encode proteomic 2DE data, please see Charleston Core Gel Ontology

The presented ontology is very simple. It consists of three owl:Classes and six rdf:Properties. Together, these vocabularies can be used to describe a protein spot on a 2DE gel. The relationship among all entities of the defined ontology, herein refered to as "cce", are summaries in Figure 1.

Figure 1: Examplatory Ontology defined in the language of DLG²

Classes

Spot

Conceptually, a "spot" of a Two Dimensional Gel Electrophoresis (2DE) experiment refers to a cluster of proteomics analytes. But for the purpose of data processing, a "spot" is defined as a closed region on the plane of 2DE gel, where the analytes reside.

Point

A cce:point defined to be a location on an assumed Cartesian plane. A cce:Point have two attributes to indicates its x-position and y-position on an implicit coordinate system of the plane.

Ellipse

Ellipse here is defined as a circle stretched along either x- or y-axis of an assumed coordinate system. The major and minor axises of an Ellipse shall be parallel to the coordinates of the implicit coordinate system (See Figure 2).

Figure 2: The definition of an Ellipse.

Properties

shape

As defined earlier that a cce:Spot is defined to be a closed region of a 2D plane, a cce:Spot therefore must assume a shape of certain kind. For the purpose of this discussion, the cce:shape of a cce:Spot must be a cce:Ellipse. Which means, the domain of cce:shape is cce:Spot and the range of cce:Spot is cce:Ellipse.

center

The cce:center refers to the center point of a cce:Ellipse. Therefore, it has an rdfs:domain of cce:Ellipse and an rdfs:range of cce:Point

x-position

An x-position is an owl:Datatype property that has a domain of cce:Point. Its value (of type xsd:double) indicates its distance from the origin on the x-axis of the assumed coordinate system.

y-position

A cce:y-position is a owl:Datatype property that has a domain of cce:Point. Its value (of type xsd:double) indicates its distance from the origin on the y-axis of the assumed coordinate system.

x-radius

A cce:x-radius is a owl:Datatype property that has a rdfs:domain of cce:Ellipse. It refers to the radius that is parallel to the x-axis of the assumed coordinate system. (see figure 2)

y-radius

A cce:y-radius is a owl:Datatype property that has a rdfs:domain of cce:Ellipse. It refers to the radius that is parallel to the y-axis of the assumed coordinate system. (see Figure 2)

The definition of this schema in RDF is located at here