Class: Proposition (Proposition)

An abstract entity representing a possible fact that is either true or false.

Comments

Propositions are taken to represent the semantic content of sentences or larger lexical entities formulated in some natural or artificial language. As abstract entities, Propositions capture a 'sharable' piece of meaning that can be put forth as true or false in many different Statement instances made by different Agents on different occasions. Their identity and existence are independent of space and time, and of whether they are ever asserted to be true by some agent.
Propositions may be used in two contexts in this model: (1) in Statements to represent the possible fact that is put forth as true, or that is subjected to an assessment of the level of evidence supporting it; (2) in Evidence Lines to represent the possible fact that an argument built from evidence items is evaluated against.

URI: sepio_linkml:Proposition

Inheritance

Entity
- Proposition

Slots

Direct slots

propositionText --> String [0..1]

A natural-language expression of the Proposition's meaning (i.e. the 'possible fact' it expresses).

subject --> String [1]

The Entity or concept about which the Proposition is made.

Implementation Guidance

* While the Core Information Model is domain-agnostic, and supports Propositions about any type of Entity, for most VA use cases, the subject will be some type of 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).

predicate --> Coding [1]

The relationship declared to hold between the subject and the object of the Proposition.

Implementation Guidance

* When applied to represent a particular type of Proposition (via 'Profiling'), implementers can define a value set of predicates for the relationships relevant in the domain - ideally using terms from community ontologies or terminologies. For example, in a 'Variant Pathogenicity Statement' Profile, the predicate value set might include terms from the GENO ontology defining 'pathogenic for condition', 'benign for condition', and 'uncertain significance for condition' relationships (GENO:0000840, GENO:0000843, GENO:0000845).

object --> String [1]

An Entity or concept that is related to the subject of a Proposition via its predicate.

Implementation Guidance

* The object of a Proposition can be any Entity or concept that is related to the subject, e.g. for Genetic Variation subjects this is often a disease, drug, gene, molecular consequence, functional impact on gene or protein.

qualifier --> Qualifier [*]

An additional piece of information that extends or refines the meaning of a Propositions's core subject - predicate - object 'triple' - by providing additional detail, or constraining the statement to apply in a particular context.

Implementation Guidance

* The qualifier attribute allows representation of more complex, n-ary propositions that may not be accommodated by a simple subject-predicate-object (SPO) triple. For example, if a 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 aspects of a Statement - e.g. for an SPO triple asserting that a 'Variant X'- causes - 'Phenotype Y', a qualifier can be used to add frequency/penetrance information that quantifies the percentage of carriers in which the phenotype is observed to manifest. Profiles of specific proposition types may define more than one qualifier, as needed to capture different types of qualifying information.
* The SEPIO core model specifies use of a key-value 'Qualifier' object to capture the meaning and value of each type of qualifying information relevant for a given type of Statement. But in practice, profiles for specific Proposition types may choose to define one or more specializations of the generic 'qualifier' property as named attributes. This makes the data more succinct and parsable, and allows specific constraints to be applied and validated for different qualifiers. For example, a VariantPathogenicityStatement profile may define a named 'alleleOriginQualifier' attribute that is required, and a named 'geneContextQualifier' attribute that is optional - both of which conceptually specialize the core-im 'qualifier' property. Under this approach, the core 'qualifier' acts as a placeholder to seed such specializations, but is not used directly in profiles.

negated --> Boolean [0..1]

A boolean flag set to 'true' to represent a negation of the proposition expressed by the subject, predicate, object, and qualifier(s) (e.g. that "Variant X is NOT pathogenic for Disease Y")

Implementation Guidance

* Along with the 'subject', predicate', 'object', and 'qualifier' attributes, the 'negated' element contributes to the semantics of the 'possible fact' that a Proposition expresses.

Inherited slots

id --> String [1]

The 'logical' identifier of the entity in the system of record, e.g. a UUID. This 'id' is unique within a given system, but may or may not be globally unique outside the system. It is used within a system to reference one object from another.

Inherited from: Entity

Implementation Guidance

* Note that it is common for implementers to create their own internal logical ids - typically a serially or randomly generated value like a UUID that is assigned to the data object as it is created in a system. But an implementer may choose to reuse an existing, globally unique id from an external system or authority for this purpose (e.g. an HGNC id for a Gene object) - as long as it is unique within the implementing system, and can be used to reference the identified object in this context.

identifiers --> String [*]

A globally-unique 'business' identifier or accession number for the real-world entity represented by a data object. These are typically assigned by an external system or authority, and used to connect entities and share content across different systems.

Inherited from: Entity

Implementation Guidance

* Preferred values for this attribute are CURIEs or URIs - so the system that provisioned the identifier is clear.
* A given real world entity - e.g. a genetic variant - may have many business identifiers defined by different systems, which can be captured in the "identifiers" property to indicate that they represent the same thing.

type --> String [1]

The name of the class that is instantiated by a data object representing the Entity.

Inherited from: Entity

Implementation Guidance

* MUST be the label of a concrete class from the data model.

label --> String [0..1]

A primary name for the Entity.

Inherited from: Entity

alternativeLabels --> String [*]

Alternative name(s) for the Entity.

Inherited from: Entity

description --> String [0..1]

A free text description of the Entity.

Inherited from: Entity

extensions --> Extension [*]

A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.

Inherited from: Entity

Implementation Guidance

* Extension objects have a key-value data structure that allows definition of custom fields in the data itself. Extensions are not expected to be natively understood, but may be used for pre-negotiated exchange of message attributes between systems.

Usages

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

Identifier and Mapping Information

Schema Source

from schema: https://w3id.org/sepio-framework/sepio-linkml

Mappings

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

LinkML Source

Direct

name: Proposition
description: An abstract entity representing a possible fact that is either true or
  false.
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 abstract
  entities, Propositions capture a 'sharable' piece of meaning that can be put forth
  as true or false in many different Statement instances made by different Agents
  on different occasions.  Their identity and existence are independent of space and
  time, and of whether they are ever asserted to be true by some agent.
- 'Propositions may be used in two contexts in this model: (1) in Statements to represent
  the possible fact that is put forth as true, or  that is subjected to an assessment
  of the level of evidence supporting it; (2) in Evidence Lines to represent the possible
  fact that an argument built from evidence items is evaluated against.'
from_schema: https://w3id.org/sepio-framework/sepio-linkml
status: Informative
is_a: Entity
attributes:
  propositionText:
    name: propositionText
    description: A natural-language expression of the Proposition's meaning (i.e.
      the 'possible fact' it expresses).
    from_schema: https://w3id.org/sepio-model
    status: Informative
    rank: 1000
    domain_of:
    - Proposition
    range: string
    required: false
    multivalued: false
  subject:
    name: subject
    description: The Entity or concept about which the Proposition is made.
    comments:
    - While the Core Information Model is domain-agnostic, and supports Propositions
      about any type of Entity, for most VA use cases, the subject will be  some type
      of 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/sepio-model
    status: Informative
    domain_of:
    - Statement
    - Proposition
    range: string
    required: true
    multivalued: false
  predicate:
    name: predicate
    description: The relationship declared to hold between the subject and the object
      of the Proposition.
    comments:
    - When applied to represent a particular type of Proposition (via 'Profiling'),
      implementers can define a value set of predicates for the relationships relevant
      in the domain - ideally using terms from community ontologies or terminologies.
      For example, in a  'Variant Pathogenicity Statement' Profile, the predicate
      value set might include terms from the GENO ontology defining  'pathogenic for
      condition', 'benign for condition', and 'uncertain significance for condition'
      relationships (GENO:0000840, GENO:0000843, GENO:0000845).
    from_schema: https://w3id.org/sepio-model
    status: Informative
    domain_of:
    - Statement
    - Proposition
    range: Coding
    required: true
    multivalued: false
  object:
    name: object
    description: An Entity or concept that is related to the subject of a Proposition
      via its predicate.
    comments:
    - The object of a Proposition can be any Entity or concept that is related to
      the subject, e.g. for Genetic Variation subjects this is often a disease, drug,
      gene, molecular consequence, functional impact on gene or protein.
    from_schema: https://w3id.org/sepio-model
    status: Informative
    domain_of:
    - Statement
    - Proposition
    range: string
    required: true
    multivalued: false
  qualifier:
    name: qualifier
    description: An additional piece of information that extends or refines the meaning
      of a Propositions's core subject - predicate - object 'triple' - by providing
      additional detail, or constraining the statement to apply in a particular context.
    comments:
    - The qualifier attribute allows representation of more complex, n-ary propositions
      that may not be accommodated by a simple subject-predicate-object (SPO) triple.
      For example, if a 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 aspects of a Statement - e.g. for an SPO triple asserting that a
      'Variant X'- causes - 'Phenotype Y', a qualifier can be used to add frequency/penetrance
      information that quantifies the percentage of carriers in which the phenotype
      is observed to manifest. Profiles of specific proposition types may define more
      than one qualifier, as needed to capture different types of qualifying information.
    - The SEPIO core model specifies use of a key-value 'Qualifier' object to capture
      the meaning and value of each type of qualifying information relevant for a
      given type of Statement. But in practice, profiles for specific Proposition
      types may choose to define one or more specializations of the generic 'qualifier'
      property as named attributes. This makes the data more succinct and parsable,
      and allows specific constraints to be applied and validated for different qualifiers.
      For example, a VariantPathogenicityStatement profile may define a named 'alleleOriginQualifier'
      attribute that is required, and a named 'geneContextQualifier' attribute that
      is optional - both of which conceptually specialize the core-im 'qualifier'
      property. Under this approach, the core 'qualifier' acts as a placeholder to
      seed such specializations, but is not used directly in profiles.
    from_schema: https://w3id.org/sepio-model
    status: Informative
    domain_of:
    - Statement
    - Proposition
    range: Qualifier
    required: false
    multivalued: true
  negated:
    name: negated
    description: A boolean flag set to 'true' to represent a negation of the proposition
      expressed by the subject, predicate, object, and qualifier(s) (e.g. that "Variant
      X is NOT pathogenic for Disease Y")
    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/sepio-model
    status: Informative
    rank: 1000
    domain_of:
    - Proposition
    range: boolean
    required: false
    multivalued: false

Induced

name: Proposition
description: An abstract entity representing a possible fact that is either true or
  false.
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 abstract
  entities, Propositions capture a 'sharable' piece of meaning that can be put forth
  as true or false in many different Statement instances made by different Agents
  on different occasions.  Their identity and existence are independent of space and
  time, and of whether they are ever asserted to be true by some agent.
- 'Propositions may be used in two contexts in this model: (1) in Statements to represent
  the possible fact that is put forth as true, or  that is subjected to an assessment
  of the level of evidence supporting it; (2) in Evidence Lines to represent the possible
  fact that an argument built from evidence items is evaluated against.'
from_schema: https://w3id.org/sepio-framework/sepio-linkml
status: Informative
is_a: Entity
attributes:
  propositionText:
    name: propositionText
    description: A natural-language expression of the Proposition's meaning (i.e.
      the 'possible fact' it expresses).
    from_schema: https://w3id.org/sepio-model
    status: Informative
    rank: 1000
    alias: propositionText
    owner: Proposition
    domain_of:
    - Proposition
    range: string
    required: false
    multivalued: false
  subject:
    name: subject
    description: The Entity or concept about which the Proposition is made.
    comments:
    - While the Core Information Model is domain-agnostic, and supports Propositions
      about any type of Entity, for most VA use cases, the subject will be  some type
      of 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/sepio-model
    status: Informative
    alias: subject
    owner: Proposition
    domain_of:
    - Statement
    - Proposition
    range: string
    required: true
    multivalued: false
  predicate:
    name: predicate
    description: The relationship declared to hold between the subject and the object
      of the Proposition.
    comments:
    - When applied to represent a particular type of Proposition (via 'Profiling'),
      implementers can define a value set of predicates for the relationships relevant
      in the domain - ideally using terms from community ontologies or terminologies.
      For example, in a  'Variant Pathogenicity Statement' Profile, the predicate
      value set might include terms from the GENO ontology defining  'pathogenic for
      condition', 'benign for condition', and 'uncertain significance for condition'
      relationships (GENO:0000840, GENO:0000843, GENO:0000845).
    from_schema: https://w3id.org/sepio-model
    status: Informative
    alias: predicate
    owner: Proposition
    domain_of:
    - Statement
    - Proposition
    range: Coding
    required: true
    multivalued: false
  object:
    name: object
    description: An Entity or concept that is related to the subject of a Proposition
      via its predicate.
    comments:
    - The object of a Proposition can be any Entity or concept that is related to
      the subject, e.g. for Genetic Variation subjects this is often a disease, drug,
      gene, molecular consequence, functional impact on gene or protein.
    from_schema: https://w3id.org/sepio-model
    status: Informative
    alias: object
    owner: Proposition
    domain_of:
    - Statement
    - Proposition
    range: string
    required: true
    multivalued: false
  qualifier:
    name: qualifier
    description: An additional piece of information that extends or refines the meaning
      of a Propositions's core subject - predicate - object 'triple' - by providing
      additional detail, or constraining the statement to apply in a particular context.
    comments:
    - The qualifier attribute allows representation of more complex, n-ary propositions
      that may not be accommodated by a simple subject-predicate-object (SPO) triple.
      For example, if a 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 aspects of a Statement - e.g. for an SPO triple asserting that a
      'Variant X'- causes - 'Phenotype Y', a qualifier can be used to add frequency/penetrance
      information that quantifies the percentage of carriers in which the phenotype
      is observed to manifest. Profiles of specific proposition types may define more
      than one qualifier, as needed to capture different types of qualifying information.
    - The SEPIO core model specifies use of a key-value 'Qualifier' object to capture
      the meaning and value of each type of qualifying information relevant for a
      given type of Statement. But in practice, profiles for specific Proposition
      types may choose to define one or more specializations of the generic 'qualifier'
      property as named attributes. This makes the data more succinct and parsable,
      and allows specific constraints to be applied and validated for different qualifiers.
      For example, a VariantPathogenicityStatement profile may define a named 'alleleOriginQualifier'
      attribute that is required, and a named 'geneContextQualifier' attribute that
      is optional - both of which conceptually specialize the core-im 'qualifier'
      property. Under this approach, the core 'qualifier' acts as a placeholder to
      seed such specializations, but is not used directly in profiles.
    from_schema: https://w3id.org/sepio-model
    status: Informative
    alias: qualifier
    owner: Proposition
    domain_of:
    - Statement
    - Proposition
    range: Qualifier
    required: false
    multivalued: true
  negated:
    name: negated
    description: A boolean flag set to 'true' to represent a negation of the proposition
      expressed by the subject, predicate, object, and qualifier(s) (e.g. that "Variant
      X is NOT pathogenic for Disease Y")
    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/sepio-model
    status: Informative
    rank: 1000
    alias: negated
    owner: Proposition
    domain_of:
    - Proposition
    range: boolean
    required: false
    multivalued: 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, but may or may not be globally
      unique outside the system. It is used within a system to reference one object
      from another.
    comments:
    - Note that it is common for implementers to create their own internal logical
      ids - typically a serially or randomly generated value like a UUID that is assigned
      to the data object as it is created in a system. But an implementer may choose
      to reuse an existing, globally unique id from an external system or authority
      for this purpose (e.g. an HGNC id for a Gene object) - as long as it is unique
      within the implementing system, and can be used to reference the identified
      object in this context.
    from_schema: https://w3id.org/sepio-model
    status: Draft
    rank: 1000
    alias: id
    owner: Proposition
    domain_of:
    - Entity
    range: string
    required: true
    multivalued: false
  identifiers:
    name: identifiers
    description: A globally-unique 'business' identifier or accession number for the
      real-world entity represented by a data object. These are typically assigned
      by an external system or authority, and used to connect entities and share content
      across different systems.
    comments:
    - Preferred values for this attribute are CURIEs or URIs - so the system that
      provisioned the identifier is clear.
    - A given real world entity - e.g. a genetic variant - may have many business
      identifiers defined by different systems, which can be captured in the "identifiers"
      property to indicate that they represent the same thing.
    from_schema: https://w3id.org/sepio-model
    status: Informative
    rank: 1000
    alias: identifiers
    owner: Proposition
    domain_of:
    - Entity
    range: string
    required: false
    multivalued: true
  type:
    name: type
    description: The name of the class that is instantiated by a data object representing
      the Entity.
    comments:
    - MUST be the label of a concrete class from the data model.
    from_schema: https://w3id.org/sepio-model
    status: Draft
    rank: 1000
    alias: type
    owner: Proposition
    domain_of:
    - Entity
    range: string
    required: true
    multivalued: false
  label:
    name: label
    description: A primary name for the Entity.
    from_schema: https://w3id.org/sepio-model
    status: Draft
    rank: 1000
    alias: label
    owner: Proposition
    domain_of:
    - Entity
    - Coding
    range: string
    required: false
    multivalued: false
  alternativeLabels:
    name: alternativeLabels
    description: Alternative name(s) for the Entity.
    from_schema: https://w3id.org/sepio-model
    status: Draft
    rank: 1000
    alias: alternativeLabels
    owner: Proposition
    domain_of:
    - Entity
    range: string
    required: false
    multivalued: true
  description:
    name: description
    description: A free text description of the Entity.
    from_schema: https://w3id.org/sepio-model
    status: Draft
    rank: 1000
    alias: description
    owner: Proposition
    domain_of:
    - Entity
    range: string
    required: false
    multivalued: false
  extensions:
    name: extensions
    description: A list of extensions to the Entity, that allow for capture of information
      not directly supported by elements defined in the model.
    comments:
    - Extension objects have a key-value data structure that allows definition of
      custom fields in the data itself. Extensions are not expected to be natively
      understood, but may be used for pre-negotiated exchange of message attributes
      between systems.
    from_schema: https://w3id.org/sepio-model
    status: Draft
    rank: 1000
    alias: extensions
    owner: Proposition
    domain_of:
    - Entity
    range: Extension
    required: false
    multivalued: true