Class: Node

UI container class extending Entity with additional information

URI: https://w3id.org/monarch/monarch-py/:Node

 classDiagram
    class Node
    click Node href "../Node"
      Entity <|-- Node
        click Entity href "../Entity"

      Node : association_counts




    Node --> "1..*" AssociationCount : association_counts
    click AssociationCount href "../AssociationCount"


      Node : category

      Node : causal_gene




    Node --> "*" Entity : causal_gene
    click Entity href "../Entity"


      Node : causes_disease




    Node --> "*" Entity : causes_disease
    click Entity href "../Entity"


      Node : deprecated

      Node : description

      Node : external_links




    Node --> "*" ExpandedCurie : external_links
    click ExpandedCurie href "../ExpandedCurie"


      Node : full_name

      Node : has_phenotype

      Node : has_phenotype_closure

      Node : has_phenotype_closure_label

      Node : has_phenotype_count

      Node : has_phenotype_label

      Node : id

      Node : in_taxon

      Node : in_taxon_label

      Node : inheritance




    Node --> "0..1" Entity : inheritance
    click Entity href "../Entity"


      Node : iri

      Node : mappings




    Node --> "*" ExpandedCurie : mappings
    click ExpandedCurie href "../ExpandedCurie"


      Node : name

      Node : namespace

      Node : node_hierarchy




    Node --> "0..1" NodeHierarchy : node_hierarchy
    click NodeHierarchy href "../NodeHierarchy"


      Node : provided_by

      Node : provided_by_link




    Node --> "0..1" ExpandedCurie : provided_by_link
    click ExpandedCurie href "../ExpandedCurie"


      Node : symbol

      Node : synonym

      Node : uri

      Node : xref

Inheritance

• Entity
  • Node

Slots

Name	Cardinality and Range	Description	Inheritance
in_taxon	0..1 String	The biolink taxon that the entity is in the closure of	direct
in_taxon_label	0..1 String	The label of the biolink taxon that the entity is in the closure of	direct
inheritance	0..1 Entity		direct
causal_gene	* Entity	A list of genes that are known to be causally associated with a disease	direct
causes_disease	* Entity	A list of diseases that are known to be causally associated with a gene	direct
mappings	* ExpandedCurie	List of ExpandedCuries with id and url for mapped entities	direct
external_links	* ExpandedCurie	ExpandedCurie with id and url for xrefs	direct
provided_by_link	0..1 ExpandedCurie	A link to the docs for the knowledge source that provided the node/edge	direct
association_counts	1..* AssociationCount		direct
node_hierarchy	0..1 NodeHierarchy		direct
id	1 String		Entity
category	0..1 String		Entity
name	0..1 String		Entity
full_name	0..1 String	The long form name of an entity	Entity
deprecated	0..1 Boolean	A boolean flag indicating that an entity is no longer considered current or v...	Entity
description	0..1 String		Entity
xref	* String		Entity
provided_by	0..1 String		Entity
symbol	0..1 String		Entity
synonym	* String		Entity
uri	0..1 String	The URI of the entity	Entity
iri	0..1 String		Entity
namespace	0..1 String	The namespace/prefix portion of this entity's identifier	Entity
has_phenotype	* String	A list of phenotype identifiers that are known to be associated with this ent...	Entity
has_phenotype_label	* String	A list of phenotype labels that are known to be associated with this entity	Entity
has_phenotype_closure	* String	A list of phenotype identifiers that are known to be associated with this ent...	Entity
has_phenotype_closure_label	* String	A list of phenotype labels that are known to be associated with this entity e...	Entity
has_phenotype_count	0..1 Integer	A count of the number of phenotypes that are known to be associated with this...	Entity

Identifier and Mapping Information

Schema Source

• from schema: https://w3id.org/monarch/monarch-py

Mappings

Mapping Type	Mapped Value
self	https://w3id.org/monarch/monarch-py/:Node
native	https://w3id.org/monarch/monarch-py/:Node

LinkML Source

Direct

name: Node
description: UI container class extending Entity with additional information
from_schema: https://w3id.org/monarch/monarch-py
is_a: Entity
slots:
- in_taxon
- in_taxon_label
- inheritance
- causal_gene
- causes_disease
- mappings
- external_links
- provided_by_link
- association_counts
- node_hierarchy

Induced

name: Node
description: UI container class extending Entity with additional information
from_schema: https://w3id.org/monarch/monarch-py
is_a: Entity
attributes:
  in_taxon:
    name: in_taxon
    description: The biolink taxon that the entity is in the closure of.
    from_schema: https://w3id.org/monarch/monarch-py
    rank: 1000
    alias: in_taxon
    owner: Node
    domain_of:
    - Entity
    - Node
    range: string
  in_taxon_label:
    name: in_taxon_label
    description: The label of the biolink taxon that the entity is in the closure
      of.
    from_schema: https://w3id.org/monarch/monarch-py
    rank: 1000
    alias: in_taxon_label
    owner: Node
    domain_of:
    - Entity
    - Node
    range: string
  inheritance:
    name: inheritance
    from_schema: https://w3id.org/monarch/monarch-py
    rank: 1000
    alias: inheritance
    owner: Node
    domain_of:
    - Node
    range: Entity
    inlined: true
  causal_gene:
    name: causal_gene
    description: A list of genes that are known to be causally associated with a disease
    from_schema: https://w3id.org/monarch/monarch-py
    rank: 1000
    alias: causal_gene
    owner: Node
    domain_of:
    - Node
    range: Entity
    multivalued: true
    inlined: true
    inlined_as_list: true
  causes_disease:
    name: causes_disease
    description: A list of diseases that are known to be causally associated with
      a gene
    from_schema: https://w3id.org/monarch/monarch-py
    rank: 1000
    alias: causes_disease
    owner: Node
    domain_of:
    - Node
    range: Entity
    multivalued: true
    inlined: true
    inlined_as_list: true
  mappings:
    name: mappings
    description: List of ExpandedCuries with id and url for mapped entities
    from_schema: https://w3id.org/monarch/monarch-py
    rank: 1000
    alias: mappings
    owner: Node
    domain_of:
    - Node
    range: ExpandedCurie
    multivalued: true
    inlined: true
    inlined_as_list: true
  external_links:
    name: external_links
    description: ExpandedCurie with id and url for xrefs
    from_schema: https://w3id.org/monarch/monarch-py
    rank: 1000
    alias: external_links
    owner: Node
    domain_of:
    - Node
    range: ExpandedCurie
    multivalued: true
    inlined: true
    inlined_as_list: true
  provided_by_link:
    name: provided_by_link
    description: A link to the docs for the knowledge source that provided the node/edge.
    from_schema: https://w3id.org/monarch/monarch-py
    rank: 1000
    alias: provided_by_link
    owner: Node
    domain_of:
    - Association
    - Node
    range: ExpandedCurie
    inlined: true
  association_counts:
    name: association_counts
    from_schema: https://w3id.org/monarch/monarch-py
    rank: 1000
    alias: association_counts
    owner: Node
    domain_of:
    - Node
    range: AssociationCount
    required: true
    multivalued: true
    inlined: true
    inlined_as_list: true
  node_hierarchy:
    name: node_hierarchy
    from_schema: https://w3id.org/monarch/monarch-py
    rank: 1000
    alias: node_hierarchy
    owner: Node
    domain_of:
    - Node
    range: NodeHierarchy
    inlined: true
  id:
    name: id
    from_schema: https://w3id.org/monarch/monarch-py
    rank: 1000
    identifier: true
    alias: id
    owner: Node
    domain_of:
    - Association
    - ExpandedCurie
    - Entity
    - HistoPheno
    - HistoBin
    - Mapping
    - MultiEntityAssociationResults
    - TermInfo
    range: string
    required: true
  category:
    name: category
    from_schema: https://w3id.org/monarch/monarch-py
    rank: 1000
    alias: category
    owner: Node
    domain_of:
    - Association
    - AssociationCount
    - CompactAssociation
    - AssociationTypeMapping
    - Entity
    range: string
    multivalued: false
  name:
    name: name
    from_schema: https://w3id.org/monarch/monarch-py
    rank: 1000
    alias: name
    owner: Node
    domain_of:
    - Entity
    - MultiEntityAssociationResults
    range: string
  full_name:
    name: full_name
    description: The long form name of an entity
    from_schema: https://w3id.org/monarch/monarch-py
    rank: 1000
    alias: full_name
    owner: Node
    domain_of:
    - Entity
    range: string
  deprecated:
    name: deprecated
    description: A boolean flag indicating that an entity is no longer considered
      current or valid.
    from_schema: https://w3id.org/monarch/monarch-py
    exact_mappings:
    - oboInOwl:ObsoleteClass
    rank: 1000
    alias: deprecated
    owner: Node
    domain_of:
    - Entity
    range: boolean
  description:
    name: description
    from_schema: https://w3id.org/monarch/monarch-py
    rank: 1000
    alias: description
    owner: Node
    domain_of:
    - Entity
    range: string
  xref:
    name: xref
    from_schema: https://w3id.org/monarch/monarch-py
    rank: 1000
    alias: xref
    owner: Node
    domain_of:
    - Entity
    range: string
    multivalued: true
  provided_by:
    name: provided_by
    from_schema: https://w3id.org/monarch/monarch-py
    rank: 1000
    alias: provided_by
    owner: Node
    domain_of:
    - Association
    - Entity
    range: string
  symbol:
    name: symbol
    from_schema: https://w3id.org/monarch/monarch-py
    rank: 1000
    alias: symbol
    owner: Node
    domain_of:
    - Entity
    range: string
  synonym:
    name: synonym
    from_schema: https://w3id.org/monarch/monarch-py
    rank: 1000
    alias: synonym
    owner: Node
    domain_of:
    - Entity
    range: string
    multivalued: true
  uri:
    name: uri
    description: The URI of the entity
    from_schema: https://w3id.org/monarch/monarch-py
    rank: 1000
    alias: uri
    owner: Node
    domain_of:
    - Entity
    range: string
  iri:
    name: iri
    from_schema: https://w3id.org/monarch/monarch-py
    rank: 1000
    alias: iri
    owner: Node
    domain_of:
    - Entity
    range: string
  namespace:
    name: namespace
    description: The namespace/prefix portion of this entity's identifier
    from_schema: https://w3id.org/monarch/monarch-py
    rank: 1000
    alias: namespace
    owner: Node
    domain_of:
    - Entity
    range: string
  has_phenotype:
    name: has_phenotype
    description: A list of phenotype identifiers that are known to be associated with
      this entity
    from_schema: https://w3id.org/monarch/monarch-py
    rank: 1000
    alias: has_phenotype
    owner: Node
    domain_of:
    - Entity
    range: string
    multivalued: true
    inlined: true
    inlined_as_list: true
  has_phenotype_label:
    name: has_phenotype_label
    description: A list of phenotype labels that are known to be associated with this
      entity
    from_schema: https://w3id.org/monarch/monarch-py
    rank: 1000
    alias: has_phenotype_label
    owner: Node
    domain_of:
    - Entity
    range: string
    multivalued: true
    inlined: true
    inlined_as_list: true
  has_phenotype_closure:
    name: has_phenotype_closure
    description: A list of phenotype identifiers that are known to be associated with
      this entity expanded to include all ancestors
    from_schema: https://w3id.org/monarch/monarch-py
    rank: 1000
    alias: has_phenotype_closure
    owner: Node
    domain_of:
    - Entity
    range: string
    multivalued: true
    inlined: true
    inlined_as_list: true
  has_phenotype_closure_label:
    name: has_phenotype_closure_label
    description: A list of phenotype labels that are known to be associated with this
      entity expanded to include all ancestors
    from_schema: https://w3id.org/monarch/monarch-py
    rank: 1000
    alias: has_phenotype_closure_label
    owner: Node
    domain_of:
    - Entity
    range: string
    multivalued: true
    inlined: true
    inlined_as_list: true
  has_phenotype_count:
    name: has_phenotype_count
    description: A count of the number of phenotypes that are known to be associated
      with this entity
    from_schema: https://w3id.org/monarch/monarch-py
    rank: 1000
    alias: has_phenotype_count
    owner: Node
    domain_of:
    - Entity
    range: integer