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Class: Proposition

An abstract entity representing the sharable meaning that can be put forth as true or false in a Statement made by an Agent.

URI: vacoreim:Proposition

classDiagram class Proposition Entity <|-- Proposition Proposition : description Proposition : extensions Proposition --|> Extension : extensions Proposition : id Proposition : identifiers Proposition : label Proposition : negated Proposition : object Proposition --|> Element : object Proposition : predicate Proposition --|> Coding : predicate Proposition : propositionText Proposition : qualifiers Proposition --|> Element : qualifiers Proposition : recordMetadata Proposition --|> RecordMetadata : recordMetadata Proposition : subject Proposition --|> Element : subject Proposition : subtype Proposition --|> Coding : subtype Proposition : type Proposition : urls Proposition : xrefs

Inheritance

Slots

Name Cardinality and Range Description Inheritance
subtype 0..1
Coding		 A specific type of proposition the Proposition object represents (e.g. a 'Variant Pathogenicity Proposition', or 'Molecular Consequence Proposition') direct
propositionText 0..1
String		 A natural-language expression of the Proposition's meaning. direct
subject 1..1
Element		 The Entity about which the Proposition is made. direct
predicate 1..1
Coding		 The relationship asserted to hold between the subject and the object of the Proposition. direct
object 1..1
Element		 An Entity, concept, or value that is related to the subject of a Proposition via its predicate. direct
qualifiers 0..*
Element		 A value or concept that extends or refines the meaning of the Proposition expressed by the core subject - predicate - object 'triple' - e.g. by providing additional information/detail, or constraining the claim to apply in a particular context. direct
negated 0..1
Boolean		 A boolean flag set to 'true' if the statement expressed by the subject, predicate, object, and qualifier(s) is explicitly asserted to be false. direct
id 1..1
Identifier		 The logical identifier of the entity in the system of record, e.g. a UUID. This 'id' is unique within a given system. The identified entity may have a different 'id' in a different system. Entity
identifiers 0..*
Identifier		 A business identifier or accession number for the entity, typically as provided by an external system or authority, that is globally unique and persists across implementing systems. Entity
label 0..1
String		 A primary name for the Entity. Entity
urls 0..*
Url		 The URL/web address of a digital resource representing the entity, or providing information about it. Entity
xrefs 0..*
String		 Cross-references to database identifier(s) representing the same (or a closely related) entity or concept as the Entity. Entity
recordMetadata 0..1
RecordMetadata		 A reusable structure that encapsulates provenance metadata about the present record/data object (as opposed to provenance information about the real world entity this record/data object represents). Entity
type 1..1
Class		 The schema class that is instantiated by the data object. Must be the name of a class from the VA schema. Element
description 0..1
String		 A free text description of the Element. Element
extensions 0..*
Extension		 A key-value data structure that allows definition of custom fields to capture information not directly supported by the VA specification. Element

Usages

used by used in type used
Statement proposition range Proposition
EvidenceLine targetProposition range Proposition

Comments

  • Propositions are taken to represent the semantic content of sentences or larger lexical entities formulated in some natural or artificial language. As primary bearers of truth, they are either true or false. They are abstract entities whose identity and existence are independent of space and time, and of whether they are ever asserted to be true by some agent.

Propositions are ‘sharable’ in the sense that the same Proposition instance can be put forth as true or false in many different Statements, as made by different Agents and/or on different occasions.

Propositions are referenced in two contexts: (1) by Statements that assert the it to be true, or describe the overall state of confidence/evidence surrounding it; (2) by Evidence Lines that report how strong an argument is made by a particular collection of evidence items for or against it.

Identifier and Mapping Information

Schema Source

  • from schema: https://w3id.org/ga4gh-va-core-im

Mappings

Mapping Type Mapped Value
self vacoreim:Proposition
native vacoreim:Proposition

LinkML Source

Direct

name: Proposition
description: An abstract entity representing the sharable meaning that can be put
  forth as true or false in a Statement made by an Agent.
title: Proposition
comments:
- "Propositions are taken to represent the semantic content of sentences or larger\
  \ lexical entities formulated in some natural or artificial language. As primary\
  \ bearers of truth, they are either true or false. They are abstract entities whose\
  \ identity and existence are independent of space and time, and of whether they\
  \ are ever asserted to be true by some agent. \n\nPropositions are ‘sharable’ in\
  \ the sense that the same Proposition instance can be put forth as true or false\
  \ in many different Statements, as made by different Agents and/or on different\
  \ occasions.\n\nPropositions are referenced in two contexts: (1) by Statements that\
  \ assert the it to be true, or describe the overall state of confidence/evidence\
  \ surrounding it; (2) by Evidence Lines that report how strong an argument is made\
  \ by a particular collection of evidence items for or against it."
from_schema: https://w3id.org/ga4gh-va-core-im
is_a: Entity
slots:
- subtype
- propositionText
- subject
- predicate
- object
- qualifiers
- negated
slot_usage:
  subtype:
    name: subtype
    description: A specific type of proposition the Proposition object represents
      (e.g. a 'Variant Pathogenicity Proposition', or 'Molecular Consequence Proposition')
    comments:
    - Use only if a profile does not define formal Proposition subclasses as part
      of the schema (in which case the generic "type" property will hold the name
      of this class that indicates the specific type of Proposition).
    multivalued: false
    domain_of:
    - DataItem
    - DataSet
    - Document
    - Statement
    - StudyResult
    - EvidenceLine
    - Method
    - Activity
    - Agent
    - Proposition
    range: Coding
    required: false
  propositionText:
    name: propositionText
    description: A natural-language expression of the Proposition's meaning.
    multivalued: false
    domain_of:
    - Proposition
    range: string
    required: false
  subject:
    name: subject
    description: The Entity about which the Proposition is made.
    comments:
    - The VA Core model is domain-agnostic, and supports statements about any type
      of Entity.  For most VA use cases, the subject will be a genetic variation -
      but data creators may want to make statements about other entities or concepts
      that represent evidence for a Statement about variation (e.g. a statement that
      a gene is valid for some disease is one type of evidence that may support the
      pathogenicity of a variant that affects that gene).
    multivalued: false
    domain_of:
    - Proposition
    range: Element
    required: true
  predicate:
    name: predicate
    description: The relationship asserted to hold between the subject and the object
      of the Proposition.
    comments:
    - The VA-Spec uses value sets to hold the types of relationships that may be described
      in a particular type of Statement. The core specification itself is domain agnostic,
      and does not define Codings for any specific types of relationships.  When applied
      to represent a particular type of Proposition (via 'Profiling'), implementers
      can define predicates for the relationships relevant in the domain. For example,
      in a Proposition concerning the pathogenicity of a variant, the predicate value
      set might include codings for 'pathogenic for', 'benign for', and 'uncertain
      significance for' relationships.
    multivalued: false
    domain_of:
    - Proposition
    range: Coding
    required: true
  object:
    name: object
    description: An Entity, concept, or value that is related to the subject of a
      Proposition via its predicate.
    comments:
    - The object of a Proposition can be an Entity that describes or is related to
      the subject Variation (e.g. a Drug, a Genetic Condition, a Study Result), a
      Coding from a value set representing some concept in the domain of discourse,
      or some quantitative value about the Variation.  'Element' covers any type of
      element in the model.
    multivalued: false
    domain_of:
    - Proposition
    range: Element
    required: true
  qualifiers:
    name: qualifiers
    description: A value or concept that extends or refines the meaning of the Proposition
      expressed by the core subject - predicate - object 'triple' - e.g. by providing
      additional information/detail, or constraining the claim to apply in a particular
      context.
    comments:
    - 'The qualifier attribute allows representation of more complex, n-ary expressions
      that may not be accommodated by a simple subject-predicate-object (SPO) triple.
      For example, if this triple asserts that ''Variant X'' - predicts sensitivity
      to - ''Treatment Y'', a qualifier can be used to indicate that this applies
      in the context of a particular ''Disease Z''.  Qualifiers can also add information
      that ''quantifies'' a Statement - e.g. for a Statement triple asserting that
      a ''Variant X''- causes - ''Phenotype Y'', a qualifier can be used to add penetrance
      information that quantifies the percentage of carriers in which the phenotype
      is observed to manifest.


      In practice, this attribute will be specialized when defining Statement Profiles
      to represent specific types of qualifying information relevant to a given Statement
      type. Some statement types may require more than one qualifier  specialization
      - each capturing a different type of information that refines or extends the
      core SPO triple. For example, a TherapeuticEfficacyStatement with a subject
      ''Variation'' and object ''Treatment''  may define a ''diseaseContextQualifier''
      and ''populationContextQualifier'' attributes to represent the disease or population
      context in which the core SPO statement applies.'
    multivalued: true
    domain_of:
    - Proposition
    range: Element
    required: false
  negated:
    name: negated
    description: A boolean flag set to 'true' if the statement expressed by the subject,
      predicate, object, and qualifier(s) is explicitly asserted to be false.
    comments:
    - Along with the 'subject', predicate', 'object', and 'qualifier' attributes,
      the 'negated' element contributes to the semantics of the 'possible fact' that
      a Proposition expresses.
    multivalued: false
    domain_of:
    - Proposition
    range: boolean
    required: false

Induced

name: Proposition
description: An abstract entity representing the sharable meaning that can be put
  forth as true or false in a Statement made by an Agent.
title: Proposition
comments:
- "Propositions are taken to represent the semantic content of sentences or larger\
  \ lexical entities formulated in some natural or artificial language. As primary\
  \ bearers of truth, they are either true or false. They are abstract entities whose\
  \ identity and existence are independent of space and time, and of whether they\
  \ are ever asserted to be true by some agent. \n\nPropositions are ‘sharable’ in\
  \ the sense that the same Proposition instance can be put forth as true or false\
  \ in many different Statements, as made by different Agents and/or on different\
  \ occasions.\n\nPropositions are referenced in two contexts: (1) by Statements that\
  \ assert the it to be true, or describe the overall state of confidence/evidence\
  \ surrounding it; (2) by Evidence Lines that report how strong an argument is made\
  \ by a particular collection of evidence items for or against it."
from_schema: https://w3id.org/ga4gh-va-core-im
is_a: Entity
slot_usage:
  subtype:
    name: subtype
    description: A specific type of proposition the Proposition object represents
      (e.g. a 'Variant Pathogenicity Proposition', or 'Molecular Consequence Proposition')
    comments:
    - Use only if a profile does not define formal Proposition subclasses as part
      of the schema (in which case the generic "type" property will hold the name
      of this class that indicates the specific type of Proposition).
    multivalued: false
    domain_of:
    - DataItem
    - DataSet
    - Document
    - Statement
    - StudyResult
    - EvidenceLine
    - Method
    - Activity
    - Agent
    - Proposition
    range: Coding
    required: false
  propositionText:
    name: propositionText
    description: A natural-language expression of the Proposition's meaning.
    multivalued: false
    domain_of:
    - Proposition
    range: string
    required: false
  subject:
    name: subject
    description: The Entity about which the Proposition is made.
    comments:
    - The VA Core model is domain-agnostic, and supports statements about any type
      of Entity.  For most VA use cases, the subject will be a genetic variation -
      but data creators may want to make statements about other entities or concepts
      that represent evidence for a Statement about variation (e.g. a statement that
      a gene is valid for some disease is one type of evidence that may support the
      pathogenicity of a variant that affects that gene).
    multivalued: false
    domain_of:
    - Proposition
    range: Element
    required: true
  predicate:
    name: predicate
    description: The relationship asserted to hold between the subject and the object
      of the Proposition.
    comments:
    - The VA-Spec uses value sets to hold the types of relationships that may be described
      in a particular type of Statement. The core specification itself is domain agnostic,
      and does not define Codings for any specific types of relationships.  When applied
      to represent a particular type of Proposition (via 'Profiling'), implementers
      can define predicates for the relationships relevant in the domain. For example,
      in a Proposition concerning the pathogenicity of a variant, the predicate value
      set might include codings for 'pathogenic for', 'benign for', and 'uncertain
      significance for' relationships.
    multivalued: false
    domain_of:
    - Proposition
    range: Coding
    required: true
  object:
    name: object
    description: An Entity, concept, or value that is related to the subject of a
      Proposition via its predicate.
    comments:
    - The object of a Proposition can be an Entity that describes or is related to
      the subject Variation (e.g. a Drug, a Genetic Condition, a Study Result), a
      Coding from a value set representing some concept in the domain of discourse,
      or some quantitative value about the Variation.  'Element' covers any type of
      element in the model.
    multivalued: false
    domain_of:
    - Proposition
    range: Element
    required: true
  qualifiers:
    name: qualifiers
    description: A value or concept that extends or refines the meaning of the Proposition
      expressed by the core subject - predicate - object 'triple' - e.g. by providing
      additional information/detail, or constraining the claim to apply in a particular
      context.
    comments:
    - 'The qualifier attribute allows representation of more complex, n-ary expressions
      that may not be accommodated by a simple subject-predicate-object (SPO) triple.
      For example, if this triple asserts that ''Variant X'' - predicts sensitivity
      to - ''Treatment Y'', a qualifier can be used to indicate that this applies
      in the context of a particular ''Disease Z''.  Qualifiers can also add information
      that ''quantifies'' a Statement - e.g. for a Statement triple asserting that
      a ''Variant X''- causes - ''Phenotype Y'', a qualifier can be used to add penetrance
      information that quantifies the percentage of carriers in which the phenotype
      is observed to manifest.


      In practice, this attribute will be specialized when defining Statement Profiles
      to represent specific types of qualifying information relevant to a given Statement
      type. Some statement types may require more than one qualifier  specialization
      - each capturing a different type of information that refines or extends the
      core SPO triple. For example, a TherapeuticEfficacyStatement with a subject
      ''Variation'' and object ''Treatment''  may define a ''diseaseContextQualifier''
      and ''populationContextQualifier'' attributes to represent the disease or population
      context in which the core SPO statement applies.'
    multivalued: true
    domain_of:
    - Proposition
    range: Element
    required: false
  negated:
    name: negated
    description: A boolean flag set to 'true' if the statement expressed by the subject,
      predicate, object, and qualifier(s) is explicitly asserted to be false.
    comments:
    - Along with the 'subject', predicate', 'object', and 'qualifier' attributes,
      the 'negated' element contributes to the semantics of the 'possible fact' that
      a Proposition expresses.
    multivalued: false
    domain_of:
    - Proposition
    range: boolean
    required: false
attributes:
  subtype:
    name: subtype
    description: A specific type of proposition the Proposition object represents
      (e.g. a 'Variant Pathogenicity Proposition', or 'Molecular Consequence Proposition')
    comments:
    - Use only if a profile does not define formal Proposition subclasses as part
      of the schema (in which case the generic "type" property will hold the name
      of this class that indicates the specific type of Proposition).
    from_schema: https://w3id.org/ga4gh-va-core-im
    rank: 1000
    multivalued: false
    alias: subtype
    owner: Proposition
    domain_of:
    - DataItem
    - DataSet
    - Document
    - Statement
    - StudyResult
    - EvidenceLine
    - Method
    - Activity
    - Agent
    - Proposition
    range: Coding
    required: false
  propositionText:
    name: propositionText
    description: A natural-language expression of the Proposition's meaning.
    from_schema: https://w3id.org/ga4gh-va-core-im
    rank: 1000
    multivalued: false
    alias: propositionText
    owner: Proposition
    domain_of:
    - Proposition
    range: string
    required: false
  subject:
    name: subject
    description: The Entity about which the Proposition is made.
    comments:
    - The VA Core model is domain-agnostic, and supports statements about any type
      of Entity.  For most VA use cases, the subject will be a genetic variation -
      but data creators may want to make statements about other entities or concepts
      that represent evidence for a Statement about variation (e.g. a statement that
      a gene is valid for some disease is one type of evidence that may support the
      pathogenicity of a variant that affects that gene).
    from_schema: https://w3id.org/ga4gh-va-core-im
    rank: 1000
    multivalued: false
    alias: subject
    owner: Proposition
    domain_of:
    - Proposition
    range: Element
    required: true
  predicate:
    name: predicate
    description: The relationship asserted to hold between the subject and the object
      of the Proposition.
    comments:
    - The VA-Spec uses value sets to hold the types of relationships that may be described
      in a particular type of Statement. The core specification itself is domain agnostic,
      and does not define Codings for any specific types of relationships.  When applied
      to represent a particular type of Proposition (via 'Profiling'), implementers
      can define predicates for the relationships relevant in the domain. For example,
      in a Proposition concerning the pathogenicity of a variant, the predicate value
      set might include codings for 'pathogenic for', 'benign for', and 'uncertain
      significance for' relationships.
    from_schema: https://w3id.org/ga4gh-va-core-im
    rank: 1000
    multivalued: false
    alias: predicate
    owner: Proposition
    domain_of:
    - Proposition
    range: Coding
    required: true
  object:
    name: object
    description: An Entity, concept, or value that is related to the subject of a
      Proposition via its predicate.
    comments:
    - The object of a Proposition can be an Entity that describes or is related to
      the subject Variation (e.g. a Drug, a Genetic Condition, a Study Result), a
      Coding from a value set representing some concept in the domain of discourse,
      or some quantitative value about the Variation.  'Element' covers any type of
      element in the model.
    from_schema: https://w3id.org/ga4gh-va-core-im
    rank: 1000
    multivalued: false
    alias: object
    owner: Proposition
    domain_of:
    - Proposition
    range: Element
    required: true
  qualifiers:
    name: qualifiers
    description: A value or concept that extends or refines the meaning of the Proposition
      expressed by the core subject - predicate - object 'triple' - e.g. by providing
      additional information/detail, or constraining the claim to apply in a particular
      context.
    comments:
    - 'The qualifier attribute allows representation of more complex, n-ary expressions
      that may not be accommodated by a simple subject-predicate-object (SPO) triple.
      For example, if this triple asserts that ''Variant X'' - predicts sensitivity
      to - ''Treatment Y'', a qualifier can be used to indicate that this applies
      in the context of a particular ''Disease Z''.  Qualifiers can also add information
      that ''quantifies'' a Statement - e.g. for a Statement triple asserting that
      a ''Variant X''- causes - ''Phenotype Y'', a qualifier can be used to add penetrance
      information that quantifies the percentage of carriers in which the phenotype
      is observed to manifest.


      In practice, this attribute will be specialized when defining Statement Profiles
      to represent specific types of qualifying information relevant to a given Statement
      type. Some statement types may require more than one qualifier  specialization
      - each capturing a different type of information that refines or extends the
      core SPO triple. For example, a TherapeuticEfficacyStatement with a subject
      ''Variation'' and object ''Treatment''  may define a ''diseaseContextQualifier''
      and ''populationContextQualifier'' attributes to represent the disease or population
      context in which the core SPO statement applies.'
    from_schema: https://w3id.org/ga4gh-va-core-im
    rank: 1000
    multivalued: true
    alias: qualifiers
    owner: Proposition
    domain_of:
    - Proposition
    range: Element
    required: false
  negated:
    name: negated
    description: A boolean flag set to 'true' if the statement expressed by the subject,
      predicate, object, and qualifier(s) is explicitly asserted to be false.
    comments:
    - Along with the 'subject', predicate', 'object', and 'qualifier' attributes,
      the 'negated' element contributes to the semantics of the 'possible fact' that
      a Proposition expresses.
    from_schema: https://w3id.org/ga4gh-va-core-im
    rank: 1000
    multivalued: false
    alias: negated
    owner: Proposition
    domain_of:
    - Proposition
    range: boolean
    required: false
  id:
    name: id
    description: The logical identifier of the entity in the system of record, e.g.
      a UUID.  This 'id' is unique within a given system. The identified entity may
      have a different 'id' in a different system.
    comments:
    - FHIR naming conventions are followed here, where an 'id' field holds logical
      identifiers which are unique only within a given system, and an 'identifier'
      field holds business identifiers, which are globally unique and used to connect
      entities and share content across systems.
    from_schema: https://w3id.org/ga4gh-va-core-im
    rank: 1000
    multivalued: false
    alias: id
    owner: Proposition
    domain_of:
    - Entity
    range: Identifier
    required: true
  identifiers:
    name: identifiers
    description: A business identifier or accession number for the entity, typically
      as provided by an external system or authority, that is globally unique and
      persists across implementing systems.
    comments:
    - FHIR naming conventions are followed here, where an 'id' field holds logical
      identifiers which are unique only within a given system, and an 'identifier'
      field holds business identifiers, which are globally unique and used to connect
      entities and share content across systems.
    from_schema: https://w3id.org/ga4gh-va-core-im
    rank: 1000
    multivalued: true
    alias: identifiers
    owner: Proposition
    domain_of:
    - Entity
    range: Identifier
    required: false
  label:
    name: label
    description: A primary name for the Entity.
    from_schema: https://w3id.org/ga4gh-va-core-im
    rank: 1000
    multivalued: false
    alias: label
    owner: Proposition
    domain_of:
    - Entity
    - Coding
    range: string
    required: false
  urls:
    name: urls
    description: The URL/web address of a digital resource representing the entity,
      or providing information about it.
    comments:
    - This attribute is meant to point directly to locations on the web where more
      information about the Entity can be found.
    from_schema: https://w3id.org/ga4gh-va-core-im
    rank: 1000
    multivalued: true
    alias: urls
    owner: Proposition
    domain_of:
    - Entity
    range: Url
    required: false
  xrefs:
    name: xrefs
    description: Cross-references to database identifier(s) representing the same
      (or a closely related) entity or concept as the Entity.
    comments:
    - Preferred values for this field are CURIEs or URLs for database records - so
      the system that provisioned the identifier is clear.
    from_schema: https://w3id.org/ga4gh-va-core-im
    rank: 1000
    multivalued: true
    alias: xrefs
    owner: Proposition
    domain_of:
    - Entity
    range: string
    required: false
  recordMetadata:
    name: recordMetadata
    description: A reusable structure that encapsulates provenance metadata about
      the present record/data object  (as opposed to provenance information about
      the real world entity this record/data object represents).
    comments:
    - Record-level metadata applies to a specific concrete encoding/serialization
      of information (e.g as a record in a specific knowlegebase, or an online digital
      resource). A RecordMetadata object can capture when, how, and by whom a specific
      record was generated or modified; what upstream resources it was derived/retrieved
      from; and record-level administrative information such as versioning and system
      / lifecycle status.
    from_schema: https://w3id.org/ga4gh-va-core-im
    rank: 1000
    multivalued: false
    alias: recordMetadata
    owner: Proposition
    domain_of:
    - Entity
    range: RecordMetadata
    required: false
  type:
    name: type
    description: The schema class that is instantiated by the data object.  Must be
      the name of a class from the VA schema.
    from_schema: https://w3id.org/ga4gh-va-core-im
    rank: 1000
    multivalued: false
    alias: type
    owner: Proposition
    domain_of:
    - Element
    range: Class
    required: true
  description:
    name: description
    description: A free text description of the Element.
    from_schema: https://w3id.org/ga4gh-va-core-im
    rank: 1000
    multivalued: false
    alias: description
    owner: Proposition
    domain_of:
    - Element
    - Extension
    range: string
    required: false
  extensions:
    name: extensions
    description: A key-value data structure that allows definition of custom fields
      to capture information not directly supported by the VA specification.
    comments:
    - The VA-Spec provides  implementers the ability to extend any model elements
      with new attributes using this flexible Extension element.
    from_schema: https://w3id.org/ga4gh-va-core-im
    rank: 1000
    multivalued: true
    alias: extensions
    owner: Proposition
    domain_of:
    - Element
    range: Extension
    required: false