CC
 

A Supplement Ontology

by Xiaoshu Wang

What is this Ontology for?

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.. The presented page is provided to offer a detailed description of how to use a supplement ontology so the examplatory ontology can be extended to describe information about virtual gels. Please note, this ontology is created for demonstrative purpose during the preparation of a manuscript. The focus is therefore neither on the completeness nor the correctness of the ontology. This ontology is designed to be simple and served only one purpose. That is to show how easy it is to extend an existing ontology in RDF. For a more complete ontology of a 2DE gel, please see CC Gel

Overview

This ontology consists of only one owl:Class and one rdf:Property. It is used to indicate a "spot" of a gel is used to construct a Virtual Gel. The ontology is summaries Figure 1.

Figure 1: Supplement Ontology

Figure 1: Supplement ontology in the syntax of DLG2

Vocabularies

VGel

A VGel is a hypothetical gel generated after aligning a series of replicate real 2DE gels. A "spot" on a VGel therefore doesn't exist in reality but its position and shape corresponds to a "spot" in another gel.

virtualGel

The owl:ObjectProperty "virtualGel" marks the correspondence between a cce:Spot and a VGel.

Note
From the perspective programming efficacy, it is perhaps a better design if the inverse relationship of the virtualGel is defined, i.e., to have a VGel composed of many VSpots, each of which coorespond to a real spot on a real gel. But again, this ontology is not designed for practical use. A more complete gel ontology can be seen from here.

Schemas

The schemas of this ontology can be retrieved from here.