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This is a high-level overview of the BEL RDF model. The model depicted here is presented to convey only the conceptual design.

BEL Resources


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.

Namespaces

Highlights the three namespaces used in our example.

Namespaces

  • Go Biological Process
  • HGNC
  • Entrez Gene

Entities

Highlights the three namespace entities used in our example.

Namespace Entities

  • apoptotic process
  • TP53
  • 7157

Namespace Properties

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 ProcessHGNC, 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/>

SELECT ?namespace

WHERE {

  ?namespace

  ?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.

Evidence

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").

Evidence

Highlights the evidence added to our example.

Equivalent Evidence

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.

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1 Comment

  1. This is a fantastic visual illustrating the RDF model. Thank you!

    I am wondering if it would be useful to show equivalence, deduction, and inference from the graph perspective. Could these visuals be applied for BEL Networks as well?

    See Glossary for an example of deduction and inference.