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 : aggregator_knowledge_sources
EdgeType : edge_properties
EdgeType : knowledge_level
EdgeType --|> KnowledgeLevelEnum : knowledge_level
EdgeType : object_categories
EdgeType : predicates
EdgeType : primary_knowledge_sources
EdgeType : qualifiers
EdgeType --|> Qualifier : qualifiers
EdgeType : source_files
EdgeType : subject_categories
EdgeType : supporting_data_sources
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 | |
| primary_knowledge_sources: The infores id(s) of the 'primary knowledge sources' for this type of edge. Note that only one primary knowledge source is allowed per edge, but there may be more than one possible value here across edges for a given type (e.g. see the infores:diseases RIG/data) |
1..* Uriorcurie |
direct | |
| supporting_data_sources: The infores id(s) of any 'supporting data sources' for this type of edge. |
* Uriorcurie |
direct | |
| aggregator_knowledge_sources: The infores id(s) of any 'aggregator_knowledge sources' for this type of edge. |
* Uriorcurie |
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: An explanation of how the source data for an edge of a particular type was generated (as rationale for why the knowledge level, agent type, and knowledge source choices for this edge type were made), along with an explanation for how/why the source data record for a particular edge was transformed into a its current Biolink edge-based representation. Note that this text will be displayed in the UI to explain the provenance of a specific edge, and should be framed accordingly. |
1 String |
direct | |
| source_files: The source file or files that provided data included in or informing edges of this type. Will usually be a single file. Multivalued because some edges are based on data that come form more than one file. If the data is ingested from a database instance or API endpoint, provide analogous information here (e.g. the name of an specific API endpoint, a database access url, or a set of tables in a database schema). |
* String |
direct | |
| additional_notes: Additional notes, considerations, or explanations of modeling patterns used for this edge type, that were not otherwise captured in dedicated fields. |
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
primary_knowledge_sources:
name: primary_knowledge_sources
description: The infores id(s) of the 'primary knowledge sources' for this type
of edge. Note that only one primary knowledge source is allowed per edge, but
there may be more than one possible value here across edges for a given type
(e.g. see the infores:diseases RIG/data)
from_schema: https://w3id.org/biolink/resource-ingest-guide-schema
domain_of:
- EdgeType
range: uriorcurie
required: true
multivalued: true
supporting_data_sources:
name: supporting_data_sources
description: The infores id(s) of any 'supporting data sources' for this type
of edge.
from_schema: https://w3id.org/biolink/resource-ingest-guide-schema
domain_of:
- EdgeType
range: uriorcurie
multivalued: true
aggregator_knowledge_sources:
name: aggregator_knowledge_sources
description: 'The infores id(s) of any ''aggregator_knowledge sources'' for this
type of edge. '
from_schema: https://w3id.org/biolink/resource-ingest-guide-schema
domain_of:
- EdgeType
range: uriorcurie
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: An explanation of how the source data for an edge of a particular
type was generated (as rationale for why the knowledge level, agent type, and
knowledge source choices for this edge type were made), along with an explanation
for how/why the source data record for a particular edge was transformed into
a its current Biolink edge-based representation. Note that this text will be
displayed in the UI to explain the provenance of a specific edge, and should
be framed accordingly.
from_schema: https://w3id.org/biolink/resource-ingest-guide-schema
domain_of:
- EdgeType
range: string
required: true
source_files:
name: source_files
description: 'The source file or files that provided data included in or informing
edges of this type. Will usually be a single file. Multivalued because some
edges are based on data that come form more than one file. If the data is ingested
from a database instance or API endpoint, provide analogous information here
(e.g. the name of an specific API endpoint, a database access url, or a set
of tables in a database schema). '
from_schema: https://w3id.org/biolink/resource-ingest-guide-schema
domain_of:
- EdgeType
range: string
multivalued: 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 fields.
from_schema: https://w3id.org/biolink/resource-ingest-guide-schema
domain_of:
- SourceInformation
- IngestInformation
- TargetInformation
- EdgeType
- NodeType
range: string