Concepts

A fundamental purpose of the ontology is to serve as a knowledge base about domain information. Within CHEMCONNECT, under the very general entity skos:Concept, from the simple knowledge organization ontology, domain concepts are defined. There are many different types of concepts used within CHEMCONNECT. The domain concepts give context to ‘keywords’ used to describe domain concepts, supply template information about domain objects (such as filling in the catalog data elements outlined previously), and to drive the user interface for clear and efficient presentation and management.

In repositories a common method to categorize objects is to allow the user to enter keywords describing the object. Those objects with the same keyword would deem to be similar. Leaving the choice of keywords free has two disadvantages. The first is though semantically two keywords would be the same, if they are not exactly the same (for a keyword match), the two similar objects would not be matched. The second disadvantage is that the interpretation of the keywords are purely from the researchers creating them and the researchers reading them. The keywords have no greater context.

Within ChemConnect, keywords are arranged in a hierarchy of Concepts (under the skos:Concept ontological object). Most of the domain information is stored as a concept. Within the hierarchy of concepts there are several types:

• Concept Keywords: These are concepts, under ChemConnectConceptProperties, within a hierarchy of concepts, with the hierarchy giving them context and meaning. The only extra information that can be associated with this type of concept are a label, for a more readable title and a comment offering a short explanation.
• Purpose Keywords: These are concepts, under the ChemConnectPurpose concept, that are a concept keyword relating to a describing purpose.
• Classification Concepts: These are concepts, under the ChemConnectClassifications concept, representing classifications. The sub-classes of these classification concepts are the specific choices of classifications (each being a concept keyword).
• Link Concepts: These are concepts associated with linking two objects, such as catalog objects. This concept can have an extra property limiting the structures it links to. This information, for example, is used by the interface to limit the choices.
• Parameter Concept: This set of concepts specifies a standardized parameter name, but also gives the template of the parameters properties.
• Observable Concept: This set of concepts give the name of standard observation data, but also specifies the observable data configuration, i.e. which parameters are needed in the observable.
• Data Structure Concept: This set of concepts define templates for catalog objects. The supplementary information in the concept fills the catalog objects with domain specific information.