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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