Class: TermPairwiseSimilarity

A simple pairwise similarity between two atomic concepts/terms

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

 classDiagram
    class TermPairwiseSimilarity
    click TermPairwiseSimilarity href "../TermPairwiseSimilarity"
      PairwiseSimilarity <|-- TermPairwiseSimilarity
        click PairwiseSimilarity href "../PairwiseSimilarity"

      TermPairwiseSimilarity : ancestor_id

      TermPairwiseSimilarity : ancestor_information_content

      TermPairwiseSimilarity : ancestor_label

      TermPairwiseSimilarity : ancestor_source

      TermPairwiseSimilarity : cosine_similarity

      TermPairwiseSimilarity : dice_similarity

      TermPairwiseSimilarity : jaccard_similarity

      TermPairwiseSimilarity : object_id

      TermPairwiseSimilarity : object_information_content

      TermPairwiseSimilarity : object_label

      TermPairwiseSimilarity : object_source

      TermPairwiseSimilarity : phenodigm_score

      TermPairwiseSimilarity : subject_id

      TermPairwiseSimilarity : subject_information_content

      TermPairwiseSimilarity : subject_label

      TermPairwiseSimilarity : subject_source

Inheritance

• PairwiseSimilarity
  • TermPairwiseSimilarity

Slots

Name	Cardinality and Range	Description	Inheritance
subject_id	1 String		direct
subject_label	0..1 String	The name of the subject entity	direct
subject_source	0..1 String	the source for the first entity	direct
object_id	1 String		direct
object_label	0..1 String	The name of the object entity	direct
object_source	0..1 String	the source for the second entity	direct
ancestor_id	0..1 Uriorcurie	the most recent common ancestor of the two compared entities	direct
ancestor_label	0..1 String	the name or label of the ancestor concept	direct
ancestor_source	0..1 String		direct
object_information_content	0..1 NegativeLogValue	The IC of the object	direct
subject_information_content	0..1 NegativeLogValue	The IC of the subject	direct
ancestor_information_content	0..1 NegativeLogValue	The IC of the object	direct
jaccard_similarity	0..1 ZeroToOne	The number of concepts in the intersection divided by the number in the union	direct
cosine_similarity	0..1 Float	the dot product of two node embeddings divided by the product of their length...	direct
dice_similarity	0..1 ZeroToOne		direct
phenodigm_score	0..1 NonNegativeFloat	the geometric mean of the jaccard similarity and the information content	direct

Usages

used by	used in	type	used
BestMatch	similarity	range	TermPairwiseSimilarity

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/:TermPairwiseSimilarity
native	https://w3id.org/monarch/monarch-py/:TermPairwiseSimilarity

LinkML Source

Direct

name: TermPairwiseSimilarity
description: A simple pairwise similarity between two atomic concepts/terms
from_schema: https://w3id.org/monarch/monarch-py
is_a: PairwiseSimilarity
slots:
- subject_id
- subject_label
- subject_source
- object_id
- object_label
- object_source
- ancestor_id
- ancestor_label
- ancestor_source
- object_information_content
- subject_information_content
- ancestor_information_content
- jaccard_similarity
- cosine_similarity
- dice_similarity
- phenodigm_score

Induced

name: TermPairwiseSimilarity
description: A simple pairwise similarity between two atomic concepts/terms
from_schema: https://w3id.org/monarch/monarch-py
is_a: PairwiseSimilarity
attributes:
  subject_id:
    name: subject_id
    from_schema: https://w3id.org/monarch/monarch-py
    rank: 1000
    alias: subject_id
    owner: TermPairwiseSimilarity
    domain_of:
    - Mapping
    - TermPairwiseSimilarity
    range: string
    required: true
  subject_label:
    name: subject_label
    description: The name of the subject entity
    from_schema: https://w3id.org/monarch/monarch-py
    rank: 1000
    is_a: name
    alias: subject_label
    owner: TermPairwiseSimilarity
    domain_of:
    - Association
    - CompactAssociation
    - AssociationTypeMapping
    - Mapping
    - TermPairwiseSimilarity
    range: string
  subject_source:
    name: subject_source
    description: the source for the first entity
    from_schema: https://w3id.org/monarch/monarch-py
    rank: 1000
    slot_uri: sssom:subject_source
    alias: subject_source
    owner: TermPairwiseSimilarity
    domain_of:
    - TermPairwiseSimilarity
    range: string
  object_id:
    name: object_id
    from_schema: https://w3id.org/monarch/monarch-py
    rank: 1000
    alias: object_id
    owner: TermPairwiseSimilarity
    domain_of:
    - Mapping
    - TermPairwiseSimilarity
    range: string
    required: true
  object_label:
    name: object_label
    description: The name of the object entity
    from_schema: https://w3id.org/monarch/monarch-py
    rank: 1000
    is_a: name
    alias: object_label
    owner: TermPairwiseSimilarity
    domain_of:
    - Association
    - CompactAssociation
    - AssociationTypeMapping
    - Mapping
    - TermPairwiseSimilarity
    range: string
  object_source:
    name: object_source
    description: the source for the second entity
    from_schema: https://w3id.org/monarch/monarch-py
    rank: 1000
    slot_uri: sssom:object_source
    alias: object_source
    owner: TermPairwiseSimilarity
    domain_of:
    - TermPairwiseSimilarity
    range: string
  ancestor_id:
    name: ancestor_id
    description: the most recent common ancestor of the two compared entities. If
      there are multiple MRCAs then the most informative one is selected
    todos:
    - decide on what to do when there are multiple possible ancestos
    from_schema: https://w3id.org/monarch/monarch-py
    rank: 1000
    alias: ancestor_id
    owner: TermPairwiseSimilarity
    domain_of:
    - TermPairwiseSimilarity
    range: uriorcurie
  ancestor_label:
    name: ancestor_label
    description: the name or label of the ancestor concept
    from_schema: https://w3id.org/monarch/monarch-py
    rank: 1000
    alias: ancestor_label
    owner: TermPairwiseSimilarity
    domain_of:
    - TermPairwiseSimilarity
    range: string
  ancestor_source:
    name: ancestor_source
    from_schema: https://w3id.org/monarch/monarch-py
    rank: 1000
    alias: ancestor_source
    owner: TermPairwiseSimilarity
    domain_of:
    - TermPairwiseSimilarity
    range: string
  object_information_content:
    name: object_information_content
    description: The IC of the object
    from_schema: https://w3id.org/monarch/monarch-py
    rank: 1000
    is_a: information_content
    alias: object_information_content
    owner: TermPairwiseSimilarity
    domain_of:
    - TermPairwiseSimilarity
    range: NegativeLogValue
  subject_information_content:
    name: subject_information_content
    description: The IC of the subject
    from_schema: https://w3id.org/monarch/monarch-py
    rank: 1000
    is_a: information_content
    alias: subject_information_content
    owner: TermPairwiseSimilarity
    domain_of:
    - TermPairwiseSimilarity
    range: NegativeLogValue
  ancestor_information_content:
    name: ancestor_information_content
    description: The IC of the object
    from_schema: https://w3id.org/monarch/monarch-py
    rank: 1000
    is_a: information_content
    alias: ancestor_information_content
    owner: TermPairwiseSimilarity
    domain_of:
    - TermPairwiseSimilarity
    range: NegativeLogValue
  jaccard_similarity:
    name: jaccard_similarity
    description: The number of concepts in the intersection divided by the number
      in the union
    from_schema: https://w3id.org/monarch/monarch-py
    rank: 1000
    is_a: score
    alias: jaccard_similarity
    owner: TermPairwiseSimilarity
    domain_of:
    - TermPairwiseSimilarity
    range: ZeroToOne
  cosine_similarity:
    name: cosine_similarity
    description: the dot product of two node embeddings divided by the product of
      their lengths
    from_schema: https://w3id.org/monarch/monarch-py
    rank: 1000
    is_a: score
    alias: cosine_similarity
    owner: TermPairwiseSimilarity
    domain_of:
    - TermPairwiseSimilarity
    range: float
  dice_similarity:
    name: dice_similarity
    from_schema: https://w3id.org/monarch/monarch-py
    rank: 1000
    is_a: score
    alias: dice_similarity
    owner: TermPairwiseSimilarity
    domain_of:
    - TermPairwiseSimilarity
    range: ZeroToOne
  phenodigm_score:
    name: phenodigm_score
    description: the geometric mean of the jaccard similarity and the information
      content
    from_schema: https://w3id.org/monarch/monarch-py
    rank: 1000
    is_a: score
    alias: phenodigm_score
    owner: TermPairwiseSimilarity
    domain_of:
    - TermPairwiseSimilarity
    range: NonNegativeFloat
    equals_expression: sqrt({jaccard_similarity} * {information_content})