Class: SemsimSearchSettings

The settings a phenotype search actually ran with, after defaults and backend routing. Every result of one search carries the same settings, so a saved response or a shared link can be reproduced.

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

 classDiagram
    class SemsimSearchSettings
    click SemsimSearchSettings href "../SemsimSearchSettings/"
      SemsimSearchSettings : default_frequency

      SemsimSearchSettings : directionality

      SemsimSearchSettings : engine

      SemsimSearchSettings : information_content

      SemsimSearchSettings : metric

      SemsimSearchSettings : search_mode

      SemsimSearchSettings : tie_break

Slots

Name	Cardinality and Range	Description	Inheritance
engine	0..1 String	The similarity backend that served the request, ducksim or semsimian	direct
metric	0..1 String	The pairwise similarity metric	direct
directionality	0..1 String	How the per-term best matches were averaged into score: subject_to_object, ...	direct
search_mode	0..1 String	hybrid prefilters candidates by set Jaccard before scoring; full scores every...	direct
information_content	0..1 String	ontology (IC from the ontology's structure) or annotation (IC from how many e...	direct
tie_break	0..1 String	none, or frequency (equal scores ordered by how frequent the matched phenotyp...	direct
default_frequency	0..1 Float	The frequency assumed for annotations that record none, used by the frequency...	direct

Usages

used by	used in	type	used
SemsimSearchResult	search_settings	range	SemsimSearchSettings

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

LinkML Source

Direct

name: SemsimSearchSettings
description: The settings a phenotype search actually ran with, after defaults and
  backend routing. Every result of one search carries the same settings, so a saved
  response or a shared link can be reproduced.
from_schema: https://w3id.org/monarch/monarch-py
attributes:
  engine:
    name: engine
    description: The similarity backend that served the request, ducksim or semsimian.
    from_schema: https://w3id.org/monarch/monarch-py-similarity
    rank: 1000
    domain_of:
    - SemsimSearchSettings
  metric:
    name: metric
    description: The pairwise similarity metric.
    from_schema: https://w3id.org/monarch/monarch-py-similarity
    domain_of:
    - TermSetPairwiseSimilarity
    - SemsimSearchSettings
  directionality:
    name: directionality
    description: 'How the per-term best matches were averaged into `score`: subject_to_object,
      object_to_subject or bidirectional.'
    from_schema: https://w3id.org/monarch/monarch-py-similarity
    rank: 1000
    domain_of:
    - SemsimSearchSettings
  search_mode:
    name: search_mode
    description: hybrid prefilters candidates by set Jaccard before scoring; full
      scores every entity in the group.
    from_schema: https://w3id.org/monarch/monarch-py-similarity
    rank: 1000
    domain_of:
    - SemsimSearchSettings
  information_content:
    name: information_content
    description: ontology (IC from the ontology's structure) or annotation (IC from
      how many entities in the searched group are annotated to the term).
    from_schema: https://w3id.org/monarch/monarch-py-similarity
    domain_of:
    - SemsimSearchSettings
  tie_break:
    name: tie_break
    description: none, or frequency (equal scores ordered by how frequent the matched
      phenotypes are in each entity).
    from_schema: https://w3id.org/monarch/monarch-py-similarity
    rank: 1000
    domain_of:
    - SemsimSearchSettings
  default_frequency:
    name: default_frequency
    description: The frequency assumed for annotations that record none, used by the
      frequency tie-break.
    from_schema: https://w3id.org/monarch/monarch-py-similarity
    rank: 1000
    domain_of:
    - SemsimSearchSettings
    range: float

Induced

name: SemsimSearchSettings
description: The settings a phenotype search actually ran with, after defaults and
  backend routing. Every result of one search carries the same settings, so a saved
  response or a shared link can be reproduced.
from_schema: https://w3id.org/monarch/monarch-py
attributes:
  engine:
    name: engine
    description: The similarity backend that served the request, ducksim or semsimian.
    from_schema: https://w3id.org/monarch/monarch-py-similarity
    rank: 1000
    alias: engine
    owner: SemsimSearchSettings
    domain_of:
    - SemsimSearchSettings
    range: string
  metric:
    name: metric
    description: The pairwise similarity metric.
    from_schema: https://w3id.org/monarch/monarch-py-similarity
    alias: metric
    owner: SemsimSearchSettings
    domain_of:
    - TermSetPairwiseSimilarity
    - SemsimSearchSettings
    range: string
  directionality:
    name: directionality
    description: 'How the per-term best matches were averaged into `score`: subject_to_object,
      object_to_subject or bidirectional.'
    from_schema: https://w3id.org/monarch/monarch-py-similarity
    rank: 1000
    alias: directionality
    owner: SemsimSearchSettings
    domain_of:
    - SemsimSearchSettings
    range: string
  search_mode:
    name: search_mode
    description: hybrid prefilters candidates by set Jaccard before scoring; full
      scores every entity in the group.
    from_schema: https://w3id.org/monarch/monarch-py-similarity
    rank: 1000
    alias: search_mode
    owner: SemsimSearchSettings
    domain_of:
    - SemsimSearchSettings
    range: string
  information_content:
    name: information_content
    description: ontology (IC from the ontology's structure) or annotation (IC from
      how many entities in the searched group are annotated to the term).
    from_schema: https://w3id.org/monarch/monarch-py-similarity
    alias: information_content
    owner: SemsimSearchSettings
    domain_of:
    - SemsimSearchSettings
    range: string
  tie_break:
    name: tie_break
    description: none, or frequency (equal scores ordered by how frequent the matched
      phenotypes are in each entity).
    from_schema: https://w3id.org/monarch/monarch-py-similarity
    rank: 1000
    alias: tie_break
    owner: SemsimSearchSettings
    domain_of:
    - SemsimSearchSettings
    range: string
  default_frequency:
    name: default_frequency
    description: The frequency assumed for annotations that record none, used by the
      frequency tie-break.
    from_schema: https://w3id.org/monarch/monarch-py-similarity
    rank: 1000
    alias: default_frequency
    owner: SemsimSearchSettings
    domain_of:
    - SemsimSearchSettings
    range: float