Table 1 Fundamental semantic objects
Semantic object | Description | Example |
|---|---|---|
Element | Represents a basic unit of a knowledge model | "Gene" element type can be used to create the "STAT3" gene element "Disease term" element type can be used to create the "pancreatic tumor" disease term element |
Relation | Describes a relationship between semantic objects | "Gene-disease" relation class can be used to create the "STAT3 is associated with disease pancreatic tumor" relation |
Annotation | Extends the properties of a semantic object by a set of attributes | Gene report Patient record Protein entry Literature abstract Experimental data (evidence) |
Experiment | Performance optimized extension of an element by a set of attributes | Expression data Metabolomics data Proteomics data |
Ontology | Classifies semantic objects according to a defined hierarchical nomenclature of concepts | "3.2.2.21 DNA-3-methaladenine glycosidase II" entry is part of the "EC numbers" ontology Gene Ontology to classify biological function NCI Thesaurus of disease terms taxonomy |
Context | Represents sets of semantic objects | Metabolic pathways Protein complexes A disease process or pattern |
Database/external object | A basic unit of a knowledge model populated from an external application/database | dbSNP Sequence Variant Genome feature |