Class: TermPairwiseSimilarity

A simple pairwise similarity between two atomic concepts/terms

URI: sim: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

Slots

Name

Cardinality and Range

Description

Inheritance

subject_id

1
Uriorcurie

The first of the two entities being compared

direct

subject_label

0..1
String

the label or name for the first entity

direct

subject_source

0..1
String

the source for the first entity

direct

object_id

0..1
Uriorcurie

The second of the two entities being compared

direct

object_label

0..1
String

the label or name for the second 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/oak/similarity

Mappings

Mapping Type

Mapped Value

self

sim:TermPairwiseSimilarity

native

sim:TermPairwiseSimilarity

LinkML Source

Direct

```yaml name: TermPairwiseSimilarity description: A simple pairwise similarity between two atomic concepts/terms from_schema: https://w3id.org/oak/similarity 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 
</details>

### Induced

<details>
```yaml
name: TermPairwiseSimilarity
description: A simple pairwise similarity between two atomic concepts/terms
from_schema: https://w3id.org/oak/similarity
is_a: PairwiseSimilarity
attributes:
  subject_id:
    name: subject_id
    description: The first of the two entities being compared
    from_schema: https://w3id.org/oak/similarity
    rank: 1000
    slot_uri: sssom:subject_id
    alias: subject_id
    owner: TermPairwiseSimilarity
    domain_of:
    - TermPairwiseSimilarity
    range: uriorcurie
    required: true
  subject_label:
    name: subject_label
    description: the label or name for the first entity
    from_schema: https://w3id.org/oak/similarity
    rank: 1000
    slot_uri: sssom:subject_label
    alias: subject_label
    owner: TermPairwiseSimilarity
    domain_of:
    - TermPairwiseSimilarity
    range: string
  subject_source:
    name: subject_source
    description: the source for the first entity
    from_schema: https://w3id.org/oak/similarity
    rank: 1000
    slot_uri: sssom:subject_source
    alias: subject_source
    owner: TermPairwiseSimilarity
    domain_of:
    - TermPairwiseSimilarity
    range: string
  object_id:
    name: object_id
    description: The second of the two entities being compared
    from_schema: https://w3id.org/oak/similarity
    rank: 1000
    slot_uri: sssom:object_id
    alias: object_id
    owner: TermPairwiseSimilarity
    domain_of:
    - TermPairwiseSimilarity
    range: uriorcurie
  object_label:
    name: object_label
    description: the label or name for the second entity
    from_schema: https://w3id.org/oak/similarity
    rank: 1000
    slot_uri: sssom:object_label
    alias: object_label
    owner: TermPairwiseSimilarity
    domain_of:
    - TermPairwiseSimilarity
    range: string
  object_source:
    name: object_source
    description: the source for the second entity
    from_schema: https://w3id.org/oak/similarity
    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/oak/similarity
    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/oak/similarity
    rank: 1000
    alias: ancestor_label
    owner: TermPairwiseSimilarity
    domain_of:
    - TermPairwiseSimilarity
    range: string
  ancestor_source:
    name: ancestor_source
    from_schema: https://w3id.org/oak/similarity
    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/oak/similarity
    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/oak/similarity
    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/oak/similarity
    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/oak/similarity
    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/oak/similarity
    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/oak/similarity
    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/oak/similarity
    rank: 1000
    is_a: score
    alias: phenodigm_score
    owner: TermPairwiseSimilarity
    domain_of:
    - TermPairwiseSimilarity
    range: NonNegativeFloat
    equals_expression: sqrt({jaccard_similarity} * {information_content})