Csolink Model

A high level datamodel of computational entities (serviceunits, errors, observable features, pathways, individuals, desired states, etc) and their associations.

Csolink Model is designed as a way of standardizing types and relational structures in knowledge graphs (KGs), where the KG may be either a property graph or RDF triple store.

The schema is expressed as a YAML, which is translated to:

• Individual pages for each class in the model, e.g https://w3id.org/csolink/vocab/Serviceunit
• An OWL ontology
• Python dataclasses, also available on PyPI
• ShEx (RDF shape constraints)
• graphql
• protobuf
• json-schema
• prefix-mapping (A simple mapping of prefix to IRI expansion)
• java classes

Datamodel

The schema assumes a property graph, where nodes represent individual entities, and edges represent relationship between entities. Csolink Model provides a schema for representing both nodes and edges.

The model itself can be divided into a few parts:

• Entities (subjects and objects)
• Predicates (relationships between core concepts)
• Associations (statements including evidence and provenance)
• Entity Slots (node properties)
• Edge Slots (edge properties)

Entities

A entity corresponds to a database entity or a concept, represented as a node in a property graph.

All typed entities are a sub-class of NamedThing.

Each entity has:

• its own unique stable URI
• mappings to other ontologies (SIO, SO, etc.)
• list of valid ID prefixes

These entity types are higher level terms that can be used to categorize nodes in a KG.

For more detailed typing, one can use specific terms from an ontology.

Associations

A typed association between two entities, usually supported by evidence and provenance. An association is represented as an edge/relationship between two nodes, in a property graph.

All edges are a sub-class of Association.

An association connects a subject node and an object node via a relation property. The nature of the association is defined based on the relation property.

Certain associations can have additional properties like provided_by, has_evidence, publications.

Slots

Slots are used to collectively refer to, both, node and edge properties.

There are two types of slots defined in the model,

• node property - all node properties are a sub-class of node property
• association slot - all edge properties are a sub-class of association slot

Browse the Csolink Model to explore all defined entities, associations, and slots.

Identifiers

See Csolink Model JSON-LD context for a list of CURIE prefix mappings.

These include prefix expansions such as:

"NCIT": "http://purl.obolibrary.org/obo/NCIT_",

Note: We do not curate these in Csolink Model. Rather we take these from upstream sources, via PrefixCommons. We specify a priority order of upstream sources in cases where conflicts may occur. See the default_curi_maps tag at the top of the csolink-model.yaml.

We also specify a small set of top-level prefix overrides via the prefixes tag at the top of the YAML.

Csolink Model representation

Csolink Model aims at representing knowledge in a graph form regardless of the graph representation used.

Following are some recommendations when attempting to use Csolink Model with each style of representation.

• Neo4J: see Mapping to Neo4j
• RDF: see Mapping to RDF

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