Class: EdgeType
Description: A structure for describing each type of edge (metaedge) created in the target knowledge graph by this ingest, including what types of edge properties it holds, and a brief explanation of why this modeling pattern was deemed appropriate to represent the source data (for display to end users in a UI system). Note that an edge type with multiple subject_category and object_category values does not mean that the full cross-product must be instantiated in the data. e.g. A KG with the edge type sub_cat: [Gene, Protein, Small Molecule], predicate: affects, obj_cat: [disease, phenotype, symptom] might include Protein-affects-Disease and Gene-affects-Symptom edges, but not include any Protein-affects-Symptom edges.
classDiagram
class EdgeType
EdgeType : additional_notes
EdgeType : agent_type
EdgeType --|> AgentTypeEnum : agent_type
EdgeType : edge_properties
EdgeType : knowledge_level
EdgeType --|> KnowledgeLevelEnum : knowledge_level
EdgeType : object_categories
EdgeType : predicates
EdgeType : qualifiers
EdgeType --|> Qualifier : qualifiers
EdgeType : subject_categories
EdgeType : ui_explanation
Slots
Name | Cardinality and Range | Inheritance | Examples |
---|---|---|---|
subject_categories: The Biolink category of the subject node of this edge type. e.g. "biolink:SmallMolecule". If two edge types differ only in their subject category, but use the same predicate, object_category, edge properties, and general provenance, they can be described together in a single NodeType object that captures the alternative subject categories. e.g. if a source provides SmallMolecule-treats-Disease and MolecularMixture-treats-Disease edge types, these can be described in a single EdgeType object with two subject categories (SmallMolecule and MolecularMixture). |
1..* Uriorcurie |
direct | |
predicates: Biolink predicate(s) that defines this type of edge. Multiple values allowed ONLY if they are a predicate and one or more of its descendent predicates (e.g. ["biolink:affects", "biolink:regulates", "biolink:disrupts"]. Otherwise, separate EdgeType objects should be created for each predicate. |
1..* Uriorcurie |
direct | |
object_categories: The Biolink category of the object node of this edge type. e.g. "biolink:Disease". If two edge types differ only in their object category, but use the same predicate, subject_category, edge properties, and general provenance, they can be described together in a single NodeType object that captures the alternative object categories. e.g. if a source provides Gene-associated_with-Disease and Gene-associated_with-PhenotypicFeature edge types, these can be described in a single EdgeType object with two subject categories (Disease and PhenotypicFeature) |
1..* Uriorcurie |
direct | |
qualifiers: If relevant, report any qualifiers applied to the edge type, as a Qualifier object that contains a qualifier_property and qualifier_range pair. e.g. the property "biolink:subject_aspect_qualifier", and range "biolink:GeneOrGeneProductOrChemicalEntityAspectEnum |
* Qualifier |
direct | |
knowledge_level: The knowledge level (or levels) relevant to this type of edge. Multivalued only if instances of this type of edge can have different knowledge levels in the data. |
1..* KnowledgeLevelEnum |
direct | |
agent_type: The agent type (or types) relevant to this type of edge. Multivalued only if instances of this type of edge can have different agent types in the data. |
1..* AgentTypeEnum |
direct | |
edge_properties: A list of one or more Biolink edge properties used in instances of this edge type in the data. |
* Uriorcurie |
direct | |
ui_explanation: A brief explanation of why this modeling pattern was deemed appropriate to represent the source data (for display to end users in a UI system). |
1 String |
direct | |
additional_notes: Additional notes, considerations, or explanations of modeling patterns used for this edge type, that were not otherwise captured in dedicated attributes. |
0..1 String |
direct |
Usages
used by | used in | type | used |
---|---|---|---|
TargetInformation | edge_type_info | range | EdgeType |
LinkML Source
name: EdgeType
description: 'A structure for describing each type of edge (metaedge) created in the
target knowledge graph by this ingest, including what types of edge properties it
holds, and a brief explanation of why this modeling pattern was deemed appropriate
to represent the source data (for display to end users in a UI system). Note that
an edge type with multiple subject_category and object_category values does not
mean that the full cross-product must be instantiated in the data. e.g. A KG with
the edge type sub_cat: [Gene, Protein, Small Molecule], predicate: affects, obj_cat:
[disease, phenotype, symptom] might include Protein-affects-Disease and Gene-affects-Symptom
edges, but not include any Protein-affects-Symptom edges.'
from_schema: https://w3id.org/biolink/resource-ingest-guide-schema
attributes:
subject_categories:
name: subject_categories
description: The Biolink category of the subject node of this edge type. e.g.
"biolink:SmallMolecule". If two edge types differ only in their subject category,
but use the same predicate, object_category, edge properties, and general provenance,
they can be described together in a single NodeType object that captures the
alternative subject categories. e.g. if a source provides SmallMolecule-treats-Disease
and MolecularMixture-treats-Disease edge types, these can be described in a
single EdgeType object with two subject categories (SmallMolecule and MolecularMixture).
from_schema: https://w3id.org/biolink/resource-ingest-guide-schema
domain_of:
- EdgeType
range: uriorcurie
required: true
multivalued: true
predicates:
name: predicates
description: 'Biolink predicate(s) that defines this type of edge. Multiple values
allowed ONLY if they are a predicate and one or more of its descendent predicates
(e.g. ["biolink:affects", "biolink:regulates", "biolink:disrupts"]. Otherwise, separate
EdgeType objects should be created for each predicate. '
from_schema: https://w3id.org/biolink/resource-ingest-guide-schema
domain_of:
- EdgeType
range: uriorcurie
required: true
multivalued: true
object_categories:
name: object_categories
description: The Biolink category of the object node of this edge type. e.g. "biolink:Disease".
If two edge types differ only in their object category, but use the same predicate,
subject_category, edge properties, and general provenance, they can be described
together in a single NodeType object that captures the alternative object categories.
e.g. if a source provides Gene-associated_with-Disease and Gene-associated_with-PhenotypicFeature
edge types, these can be described in a single EdgeType object with two subject
categories (Disease and PhenotypicFeature)
from_schema: https://w3id.org/biolink/resource-ingest-guide-schema
domain_of:
- EdgeType
range: uriorcurie
required: true
multivalued: true
qualifiers:
name: qualifiers
description: If relevant, report any qualifiers applied to the edge type, as a
Qualifier object that contains a qualifier_property and qualifier_range pair.
e.g. the property "biolink:subject_aspect_qualifier", and range "biolink:GeneOrGeneProductOrChemicalEntityAspectEnum
from_schema: https://w3id.org/biolink/resource-ingest-guide-schema
domain_of:
- EdgeType
range: Qualifier
multivalued: true
knowledge_level:
name: knowledge_level
description: The knowledge level (or levels) relevant to this type of edge. Multivalued
only if instances of this type of edge can have different knowledge levels in
the data.
from_schema: https://w3id.org/biolink/resource-ingest-guide-schema
domain_of:
- EdgeType
range: KnowledgeLevelEnum
required: true
multivalued: true
agent_type:
name: agent_type
description: The agent type (or types) relevant to this type of edge. Multivalued
only if instances of this type of edge can have different agent types in the
data.
from_schema: https://w3id.org/biolink/resource-ingest-guide-schema
domain_of:
- EdgeType
range: AgentTypeEnum
required: true
multivalued: true
edge_properties:
name: edge_properties
description: A list of one or more Biolink edge properties used in instances of
this edge type in the data.
from_schema: https://w3id.org/biolink/resource-ingest-guide-schema
domain_of:
- EdgeType
range: uriorcurie
multivalued: true
ui_explanation:
name: ui_explanation
description: A brief explanation of why this modeling pattern was deemed appropriate
to represent the source data (for display to end users in a UI system).
from_schema: https://w3id.org/biolink/resource-ingest-guide-schema
domain_of:
- EdgeType
range: string
required: true
additional_notes:
name: additional_notes
description: Additional notes, considerations, or explanations of modeling patterns
used for this edge type, that were not otherwise captured in dedicated attributes.
from_schema: https://w3id.org/biolink/resource-ingest-guide-schema
domain_of:
- SourceInformation
- IngestInformation
- TargetInformation
- EdgeType
- NodeType
range: string