Mapping Biolink Model to a RDF and RDF*

This document describes how Biolink is to be used in the context of RDF, either in storage in a triplestore, or in serialization to one of the RDF syntaxes, such as turtle.

In RDF, a graph is a collection of triples <S P O> (subject predicate object). The S and P must be RDF resources (nodes). The O can be a literal or a resource.

Graphs are organized into collections of Named Graphs. Each triple can be conceived of as a quad <S P O G>.

Node and node properties

Each node in a graph corresponds to an RDF resource.

Biolink Model defines a typology of nodes, all of which inherit from biolink:NamedThing.

Core properties for a node:

The biolink:id MUST be provided and MUST be a CURIE, which maps to the resource IRI/URI using a standard prefix expansion. The RDF graph MAY include the CURIE short-form represented with the predicate dcterms:identifier where the CURIE itself is a literal.

The biolink:name field SHOULD correspond to a concise label for the entity, and maps to rdfs:label.

For example, the biolink node with ID MONDO:0001083 and name Fanconi syndrome will be expressed in RDF (turtle syntax) as:

PREFIX rdfs: <> 

MONDO:0001083 rdfs:label "Fanconi syndrome"

When the CURIEs are expanded this will be rendered as:

<> <> "Fanconi syndrome" .

Types and Categories

To define the type of a node, you can use the rdf:type to link to a specific node type. You MAY use the predicate biolink:category to represent additional categories for that node.

The rdf:type triples MAY be partitioned into separate named graphs. For example, it can be convenient to put the direct rdf:type assertion in the main graph and the inferred/index (ie asserted plus inferred) in a separate ‘inferred’ graph.

Additional node properties

You MAY provide as many additional properties as required. These SHOULD come from a registered list of properties for that node type.

Edge and edge properties

An edge maps to an RDF triple where both the subject and object are nodes representing Biolink entities.

RDF reification is used for representing edge properties. RDF* provides a convenient syntax for abstracting over this.

So for example, an edge between x and y with edge label p and an additional edge property publication=PMID:123 would be represented in RDF* as:

:x :p :y <<bl:publication>>

This is syntactic sugar for the more verbose reification triples:

:x :p :y .
[a rdf:Statement ;
   rdf:subject :x ;
   rdf:predicate :p ;
   rdf:object :y ;
   bl:publication ].

See biolink:Association for a taxonomy of associations defined by the model, and to see a list of generic properties that are associated with an edge.

Comparison to Neo4J mapping

The mapping is similar to Mapping to Neo4j. Differences include:

  • Neo4j uses a Property Graph (PG) model. In RDF reification is used. RDF* provides a PG later
  • In the Neo4J mapping, ids are represented as CURIEs. In RDF URIs are first class entities.
  • There is a built-in concept of category in Neo4j, called labels. In RDF this is modeled as another node property (rdf:type)