Charleston Core 2D Gel Ontology(CC2GO)
by Xiaoshu Wang
Introduction
The Charleston Core 2D Gel Ontology (CC2GO) defines concepts that can be used to drive the semantic access of a two-dimensional gel experiment. CC2GO defines the data semantics for the basic vocabularies that are used daily by web-bench scientists, such as "Gel" and "Spot". Our previous design CCGel tried to do too much with one ontology, unnecessarily making the ontological terms difficult to understand. In this version, instead of trying to accommodate different kind of gel, we made it clear what the Gel and Spot is actually is. The overall design of the ontology is shown in Fig. 1.
Figure 1 The Design of CC2GO in DLG2
Vocabularies
Classes
Gel
A cc2go:Gel is an abstract concept of processed gel information. It is not the actual gel made of the acrylamide that run by the web scientist. Neither is it the image taken afterwards. A cc2go:Gel is an abstract concept that is made of a collection of spots (cc2go:Spot) as the result of a series of image processing algorithm. A cc2go:Gel is by this definition a virtual concepts.
RGel
Conceptualization
The cc2go:RGel is created to represent those Gel information that results from the direct image processing algorithm. Hence, each cc2go:RGel should have a corresponding image.
Class relationships
A cc2go:RGel is an rdfs:subClassOf cc2go:Gel.
Restrictions
No more one image can be associated with a cc2go:RGel. The minimal cardinality is not set to give some leniency to lasy developers.
Spot
Conceptualization
A cc2go:Spot is the abstract representation of a small region on a cc2go:Gel, usually resulted from aggregated protein analytes on a real actually gel that result in the change of some wavelenght emisison change comparing to its surrounding environment. A cc2go:Spot is usually assigned a numeric value to indicate "mw", "pi", "intensity" by the image software along with a location and shape.
Restrictions
A cc2go:Spot must have one and only one of the following properties, cc2go:mw, cc2go:pi, cc2go:intensity, cc2go:location, and cc2go:shape.
Properties
hasSpot
The cc2go:hasSpot is a property to indicate the relationship between a Gel and Spots. The domain of cc2go:hasSpot is a cc2go:Gel and the range of it is cc2go:Spot.
fromGel
The cc2go:fromGel is a property to indicate the relationship between a Spot and a Gel. The domain of cc2go:fromGel is a cc2go:Spot and the range of it is cc2go:RGel.
mw
The cc2go:mw is a owl:DatatypeProperty of type xsd:double. It is the place holder for the numeric value of molecular weight that an image analysis program assigned to a spot.
The rdfs:domain of cc2go:mw is cc2go:Spot
pi
The cc2go:pi is a owl:DatatypeProperty of type xsd:double. It is the place holder for the numeric value of pI that an image analysis program assigned to a spot.
The rdfs:domain of cc2go:pi is cc2go:Spot
intensity
The cc2go:intensity is a owl:DatatypeProperty of type xsd:double. It is the place holder for the numeric value of spot intensity that an image analysis program assigned to a spot.
The rdfs:domain of cc2go:intensity is cc2go:Spot
location
The cc2go:location indicate the location of a spot on a presumed 2D coordinate place.
The rdfs:domain of cc2go:location is cc2go:Spot. The range is unspecified because CC2GO will usually used in conjunction with a 2D geometry ontology so it is left to the application profile.
shape
The cc2go:shape indicate the location of a spot on a presumed 2D coordinate place.
The rdfs:domain of cc2go:shape is cc2go:Spot. The range is unspecified because CC2GO will usually used in conjunction with a 2D geometry ontology so it is left to the application profile.