This is a high-level overview of the BEL RDF model. The model depicted here is presented to convey only the conceptual design.
Namespaces and Entities
Shows three namespace entities and the namespaces that contain them. The SKOS vocabulary inScheme property identifies which namespace an entity belongs to. The exactMatch property indicates an entity is equivalent to another.
Highlights the three namespaces used in our example.
- Go Biological Process
- Entrez Gene
Highlights the three namespace entities used in our example.
- apoptotic process
A closer look at a namespace reveals additional properties. The instance of property for each namespace is supported by the rdf:type property. The belv properties define a category of semantic properties specific to BEL.
To further illustrate this model, Go Biological Process, HGNC, and Entrez Gene define the complete set of BEL namespaces described by this model. This set is described by the following SPARQL query.
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX belv: <http://www.openbel.org/bel/vocabulary/>
?namespace a belv:NamespaceConceptScheme.
Namespace Entity Properties
A closer look at namespace entities reveals additional properties. Each namespace property in this example is categorized as either a Biological Process or a protein-coding abundance (Abundance, Gene, Protein, RNA). You can also see alternate labels associated with each entity. The identifier 0006915 is commonly known as apoptotic process, in the namespace to which this entity belongs.
This example adds two pieces of evidence into the RDF model, i.e., the BEL statements
p(HGNC:TP53) increases bp(GOBP:"apoptotic process") and
p(EGID:7157) increases bp(GOBP:"apoptotic process").
Highlights the evidence added to our example.
Though not identical, the two BEL statements in this example are equivalent. Following the green, orange, and blue arrows emanating from the statement on the right highlights the paths that establish the equivalence.