Class: Entity

Post-closurize node shape (entity + closure expansion + per-predicate aggregations).

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

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

      Entity : broad_synonym

      Entity : category

      Entity : deprecated

      Entity : description

      Entity : exact_synonym

      Entity : file_source

      Entity : full_name

      Entity : has_attribute

      Entity : has_biological_sex

      Entity : has_descendant

      Entity : has_descendant_count

      Entity : has_descendant_label

      Entity : has_gene

      Entity : has_phenotype

      Entity : has_phenotype_closure

      Entity : has_phenotype_closure_label

      Entity : has_phenotype_count

      Entity : has_phenotype_label

      Entity : id

      Entity : in_taxon

      Entity : in_taxon_label

      Entity : iri

      Entity : name

      Entity : namespace

      Entity : narrow_synonym

      Entity : provided_by

      Entity : related_synonym

      Entity : same_as

      Entity : subsets

      Entity : symbol

      Entity : synonym

      Entity : synonyms

      Entity : type

      Entity : xref

Inheritance

• Entity
  • Node
  • SearchResult

Slots

Name	Cardinality and Range	Description	Inheritance
id	1 String		direct
category	0..1 String		direct
name	0..1 String		direct
description	0..1 String		direct
xref	* String		direct
synonym	* String		direct
exact_synonym	* String	An exact synonym for the entity	direct
broad_synonym	* String	A broader synonym for the entity	direct
narrow_synonym	* String	A narrower synonym for the entity	direct
related_synonym	* String	A related synonym for the entity	direct
deprecated	0..1 Boolean	A boolean flag indicating that an entity is no longer considered current or v...	direct
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
iri	0..1 String		direct
same_as	* String		direct
subsets	* String	A list of subsets that the entity belongs to	direct
file_source	0..1 String	Source file stem injected by koza at load time	direct
provided_by	0..1 String		direct
full_name	0..1 String	The long form name of an entity	direct
symbol	0..1 String		direct
type	0..1 String	The type of the entity (e	direct
has_attribute	* Uriorcurie		direct
has_biological_sex	0..1 String	The biological sex of an individual entity	direct
synonyms	0..1 String		direct
has_gene	* Uriorcurie		direct
namespace	0..1 String	The namespace/prefix portion of this entity's identifier	direct
has_phenotype	* String	A list of phenotype identifiers that are known to be associated with this ent...	direct
has_phenotype_label	* String	A list of phenotype labels that are known to be associated with this entity	direct
has_phenotype_count	0..1 Integer	A count of the number of phenotypes that are known to be associated with this...	direct
has_phenotype_closure	* String	A list of phenotype identifiers that are known to be associated with this ent...	direct
has_phenotype_closure_label	* String	A list of phenotype labels that are known to be associated with this entity e...	direct
has_descendant	* String	A list of entity identifiers that are known to be descendants of this entity	direct
has_descendant_label	* String	A list of entity labels that are known to be descendants of this entity	direct
has_descendant_count	0..1 Integer	A count of the number of entities that are known to be descendants of this en...	direct

Usages

used by	used in	type	used
EntityResults	items	range	Entity
Node	inheritance	range	Entity
Node	causal_gene	range	Entity
Node	causes_disease	range	Entity
CrossSpeciesTermClique	root_term	range	Entity
CrossSpeciesTermClique	clique_entities	range	Entity
NodeHierarchy	super_classes	range	Entity
NodeHierarchy	sub_classes	range	Entity
TextAnnotationResult	tokens	range	Entity
SemsimSearchResult	subject	range	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/Entity
native	https://w3id.org/monarch/monarch-py/Entity

LinkML Source

Direct

name: Entity
description: Post-closurize node shape (entity + closure expansion + per-predicate
  aggregations).
from_schema: https://w3id.org/monarch/monarch-py
slots:
- id
- category
- name
- description
- xref
- synonym
- exact_synonym
- broad_synonym
- narrow_synonym
- related_synonym
- deprecated
- in_taxon
- in_taxon_label
- iri
- same_as
- subsets
- file_source
- provided_by
- full_name
- symbol
- type
- has_attribute
- has_biological_sex
- synonyms
- has_gene
- namespace
- has_phenotype
- has_phenotype_label
- has_phenotype_count
- has_phenotype_closure
- has_phenotype_closure_label
- has_descendant
- has_descendant_label
- has_descendant_count

Induced

name: Entity
description: Post-closurize node shape (entity + closure expansion + per-predicate
  aggregations).
from_schema: https://w3id.org/monarch/monarch-py
attributes:
  id:
    name: id
    from_schema: https://w3id.org/monarch/monarch-py
    rank: 1000
    identifier: true
    alias: id
    owner: Entity
    domain_of:
    - ExpandedCurie
    - HistoPheno
    - HistoBin
    - Mapping
    - MultiEntityAssociationResults
    - CaseEntity
    - CasePhenotype
    - HistoPhenoBin
    - CasePhenotypeCellData
    - GridColumnEntity
    - GridRowEntity
    - GridBin
    - Qualifier
    - GridCellData
    - TermInfo
    - Entity
    - Association
    range: string
    required: true
  category:
    name: category
    from_schema: https://w3id.org/monarch/monarch-py
    rank: 1000
    alias: category
    owner: Entity
    domain_of:
    - AssociationCount
    - CompactAssociation
    - AssociationTypeMapping
    - GridColumnEntity
    - GridRowEntity
    - Entity
    - Association
    range: string
    multivalued: false
  name:
    name: name
    from_schema: https://w3id.org/monarch/monarch-py
    rank: 1000
    alias: name
    owner: Entity
    domain_of:
    - MultiEntityAssociationResults
    - Entity
    range: string
  description:
    name: description
    from_schema: https://w3id.org/monarch/monarch-py
    rank: 1000
    alias: description
    owner: Entity
    domain_of:
    - Entity
    range: string
  xref:
    name: xref
    from_schema: https://w3id.org/monarch/monarch-py
    rank: 1000
    alias: xref
    owner: Entity
    domain_of:
    - Entity
    range: string
    multivalued: true
  synonym:
    name: synonym
    from_schema: https://w3id.org/monarch/monarch-py
    rank: 1000
    alias: synonym
    owner: Entity
    domain_of:
    - Entity
    range: string
    multivalued: true
  exact_synonym:
    name: exact_synonym
    description: An exact synonym for the entity
    from_schema: https://w3id.org/monarch/monarch-py
    rank: 1000
    alias: exact_synonym
    owner: Entity
    domain_of:
    - Entity
    range: string
    multivalued: true
  broad_synonym:
    name: broad_synonym
    description: A broader synonym for the entity
    from_schema: https://w3id.org/monarch/monarch-py
    rank: 1000
    alias: broad_synonym
    owner: Entity
    domain_of:
    - Entity
    range: string
    multivalued: true
  narrow_synonym:
    name: narrow_synonym
    description: A narrower synonym for the entity
    from_schema: https://w3id.org/monarch/monarch-py
    rank: 1000
    alias: narrow_synonym
    owner: Entity
    domain_of:
    - Entity
    range: string
    multivalued: true
  related_synonym:
    name: related_synonym
    description: A related synonym for the entity
    from_schema: https://w3id.org/monarch/monarch-py
    rank: 1000
    alias: related_synonym
    owner: Entity
    domain_of:
    - Entity
    range: string
    multivalued: true
  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: Entity
    domain_of:
    - Entity
    range: boolean
  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: Entity
    domain_of:
    - Node
    - Entity
    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: Entity
    domain_of:
    - Node
    - Entity
    range: string
  iri:
    name: iri
    from_schema: https://w3id.org/monarch/monarch-py
    rank: 1000
    alias: iri
    owner: Entity
    domain_of:
    - Entity
    range: string
  same_as:
    name: same_as
    from_schema: https://w3id.org/monarch/monarch-py
    rank: 1000
    alias: same_as
    owner: Entity
    domain_of:
    - Entity
    range: string
    multivalued: true
  subsets:
    name: subsets
    description: A list of subsets that the entity belongs to
    from_schema: https://w3id.org/monarch/monarch-py
    rank: 1000
    alias: subsets
    owner: Entity
    domain_of:
    - Entity
    range: string
    multivalued: true
  file_source:
    name: file_source
    description: Source file stem injected by koza at load time.
    from_schema: https://w3id.org/monarch/monarch-py
    rank: 1000
    alias: file_source
    owner: Entity
    domain_of:
    - Entity
    - Association
    range: string
    multivalued: false
  provided_by:
    name: provided_by
    from_schema: https://w3id.org/monarch/monarch-py
    rank: 1000
    alias: provided_by
    owner: Entity
    domain_of:
    - Entity
    - Association
    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: Entity
    domain_of:
    - Entity
    range: string
  symbol:
    name: symbol
    from_schema: https://w3id.org/monarch/monarch-py
    rank: 1000
    alias: symbol
    owner: Entity
    domain_of:
    - Entity
    range: string
  type:
    name: type
    description: The type of the entity (e.g. sequence onotology type for genes etc)
    from_schema: https://w3id.org/monarch/monarch-py
    rank: 1000
    alias: type
    owner: Entity
    domain_of:
    - Entity
    range: string
  has_attribute:
    name: has_attribute
    from_schema: https://w3id.org/monarch/monarch-py
    exact_mappings:
    - biolink:has_attribute
    rank: 1000
    slot_uri: biolink:has_attribute
    alias: has_attribute
    owner: Entity
    domain_of:
    - Entity
    - Association
    range: uriorcurie
    multivalued: true
  has_biological_sex:
    name: has_biological_sex
    description: The biological sex of an individual entity.
    from_schema: https://w3id.org/monarch/monarch-py
    rank: 1000
    alias: has_biological_sex
    owner: Entity
    domain_of:
    - Node
    - Entity
    range: string
  synonyms:
    name: synonyms
    from_schema: https://w3id.org/monarch/monarch-py
    rank: 1000
    alias: synonyms
    owner: Entity
    domain_of:
    - Entity
    range: string
  has_gene:
    name: has_gene
    from_schema: https://w3id.org/monarch/monarch-py
    exact_mappings:
    - biolink:has_gene
    rank: 1000
    slot_uri: biolink:has_gene
    alias: has_gene
    owner: Entity
    domain_of:
    - Entity
    range: uriorcurie
    multivalued: true
  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: Entity
    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: Entity
    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: Entity
    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: Entity
    domain_of:
    - Entity
    range: integer
  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: Entity
    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: Entity
    domain_of:
    - Entity
    range: string
    multivalued: true
    inlined: true
    inlined_as_list: true
  has_descendant:
    name: has_descendant
    description: A list of entity identifiers that are known to be descendants of
      this entity
    from_schema: https://w3id.org/monarch/monarch-py
    rank: 1000
    alias: has_descendant
    owner: Entity
    domain_of:
    - Entity
    range: string
    multivalued: true
    inlined: true
    inlined_as_list: true
  has_descendant_label:
    name: has_descendant_label
    description: A list of entity labels that are known to be descendants of this
      entity
    from_schema: https://w3id.org/monarch/monarch-py
    rank: 1000
    alias: has_descendant_label
    owner: Entity
    domain_of:
    - Entity
    range: string
    multivalued: true
    inlined: true
    inlined_as_list: true
  has_descendant_count:
    name: has_descendant_count
    description: A count of the number of entities that are known to be descendants
      of this entity
    from_schema: https://w3id.org/monarch/monarch-py
    rank: 1000
    alias: has_descendant_count
    owner: Entity
    domain_of:
    - Entity
    range: integer