FAQ

How do I type nodes in a graph with concepts that are not in the Biolink Model?

Each node in a knowledge graph can be typed using the slot category.

In addition to category, one can type a node using the rdf:type and rdfs:subClassOf predicates.

How do I type edges in a graph with concepts that are not in the Biolink Model?

Each edge in a knowledge graph can be typed using the slot category.

In addition to category, one can type a node using the rdf:type.

How do I add properties that are not in the Biolink Model

Each node and/or edge can have properties that are outside of Biolink Model.

Alternatively, for a more structured representation it is recommended to use the class Attribute to represent the property and link a node/edge using the has attribute slot.

What is the serialized form of Biolink Model?

Refer to Working with the Model for an example on how a Biolink Model graph can be represented as labelled property graphs and RDF graphs.

What is the difference between predicate, relation, category?

• predicate is an association slot and must have a value from the related to hierarchy
• relation is an association slot and can have a value from any external ontology, controlled vocabulary, thesauri, or taxonomy
• category (or rdf:type) is a slot and must have a value from the named thing or the association hierarchy.