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Generate new version of the linkml model for assertion_evidence
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‎linkml-schema/assertion_evidence.yaml‎

Lines changed: 117 additions & 69 deletions
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@@ -12,6 +12,7 @@ prefixes:
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prov: http://www.w3.org/ns/prov#
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eco: http://purl.obolibrary.org/obo/ECO_
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sepio: http://purl.obolibrary.org/obo/SEPIO_
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oa: http://www.w3.org/ns/oa#
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default_prefix: brainkb
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default_range: string
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enums:
@@ -71,6 +72,11 @@ enums:
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permissible_values:
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Clinical: {}
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NonClinical: {}
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AssertionMethod:
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from_schema: https://identifiers.org/brain-bican/assertion-evidence-schema
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permissible_values:
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AutomaticAssertion: {}
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ManualAssertion: {}
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slots:
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uses:
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description: The eco:uses property is the inverse of the eco:used_in property
@@ -92,68 +98,22 @@ slots:
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range: AssertionMethod
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is_associated_with:
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from_schema: https://identifiers.org/brain-bican/assertion-evidence-schema
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has_data_annotation:
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has_annotation:
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from_schema: https://identifiers.org/brain-bican/assertion-evidence-schema
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classes:
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Assertion:
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description: A statement made by a particular agent on a particular occasion that
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a particular proposition is true, based on the evaluation of one or more lines
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of evidence.
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has_summary:
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from_schema: https://identifiers.org/brain-bican/assertion-evidence-schema
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slots:
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- has_assertion_method
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- is_associated_with
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- has_data_annotation
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slot_usage:
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has_assertion_method:
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description: The brainkb:hasAssertionMethod property relates an eco:Assertion
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to an brainkb:AssertionMethod that differentiates different types of assertions
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techniques used while making an assertion.
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is_associated_with:
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description: The brainkb:isAssociatedWith property establishes relationships
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between different entities:it links sepio:Assertion to brainkb:AssertionSummary,
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indicating the association between an assertion and its corresponding summary.
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range: AssertionSummary
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has_data_annotation:
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range: DataAnnotation
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attributes:
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has_assertion_category:
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description: The brainkb:hasAssertionCategory property relates brainkb:Evidence
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and brainkb:Categories, specifying the classification or category that the
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assertion belongs to.
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from_schema: https://identifiers.org/brain-bican/assertion-evidence-schema
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slot_uri: brainkb:hasAssertionCategory
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alias: hasAssertionCategory
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range: Categories
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has_assertion_text:
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description: The brainkb:hasAssertionText property relates an eco:Assertion
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to an xsd:string, providing a textual excerpt of the assertion being made.
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from_schema: https://identifiers.org/brain-bican/assertion-evidence-schema
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slot_uri: brainkb:hasAssertionText
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alias: hasAssertionText
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range: string
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has_assertion_method:
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description: The brainkb:hasAssertionMethod property relates an eco:Assertion
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to an eco:assertion method that differentiates different types of assertions
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techniques used while making an assertion.
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from_schema: https://identifiers.org/brain-bican/assertion-evidence-schema
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slot_uri: brainkb:hasAssertionMethod
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alias: hasAssertionMethod
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range: AssertionMethod
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class_uri: sepio:Assertion
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Document:
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description: A collection of information content entities intended to be understood
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together as a whole
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has_evidence_line:
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from_schema: https://identifiers.org/brain-bican/assertion-evidence-schema
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class_uri: sepio:Document
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is_expressed_in:
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from_schema: https://identifiers.org/brain-bican/assertion-evidence-schema
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is_described_by:
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from_schema: https://identifiers.org/brain-bican/assertion-evidence-schema
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classes:
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Activity:
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description: An activity is something that occurs over a period of time and acts
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upon or with entities; it may include consuming, processing, transforming, modifying,
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relocating, using, or generating entities.
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from_schema: https://identifiers.org/brain-bican/assertion-evidence-schema
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attributes:
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ended_at_time:
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description: The prov:endedAtTime establishes the relationship between prov:Activity
@@ -181,13 +141,97 @@ classes:
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between different entities: it connects prov:Agent to prov:Activity, reflecting
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the involvement or connection between an agent and an activity.'
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range: Activity
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class_uri: prov:Agent
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Annotation:
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description: An annotation is a written explanatory or critical description, or
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other in-context information (e.g., pattern, motif, link), that has been associated
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with data or other types of information.
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from_schema: https://identifiers.org/brain-bican/assertion-evidence-schema
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attributes:
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cell_annotation:
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from_schema: https://identifiers.org/brain-bican/assertion-evidence-schema
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slot_uri: brainkb:cellAnnotation
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alias: cellAnnotation
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range: string
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description:
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from_schema: https://identifiers.org/brain-bican/assertion-evidence-schema
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slot_uri: brainkb:description
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alias: description
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range: string
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class_uri: oa:Annotation
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Assertion:
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description: A statement made by a particular agent on a particular occasion that
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a particular proposition is true, based on the evaluation of one or more lines
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of evidence.
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from_schema: https://identifiers.org/brain-bican/assertion-evidence-schema
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slots:
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- has_annotation
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- has_assertion_method
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- has_summary
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- has_evidence_line
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- is_expressed_in
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slot_usage:
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has_annotation:
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slot_uri: sio:hasAnnotation
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range: Annotation
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has_assertion_method:
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description: The brainkb:hasAssertionMethod property relates an eco:Assertion
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to an brainkb:AssertionMethod that differentiates different types of assertions
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techniques used while making an assertion.
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has_summary:
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slot_uri: brainkb:hasSummary
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alias: hasSummary
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range: AssertionSummary
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has_evidence_line:
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description: A relationship between an assertion or proposition and an evidence
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line used in evaluating its validity.
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slot_uri: sepio:hasEvidenceLine
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range: EvidenceLine
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is_expressed_in:
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slot_uri: sepio:is_expressed_in
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range: Document
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attributes:
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has_assertion_category:
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description: The brainkb:hasAssertionCategory property relates brainkb:Evidence
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and brainkb:Categories, specifying the classification or category that the
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assertion belongs to.
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from_schema: https://identifiers.org/brain-bican/assertion-evidence-schema
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slot_uri: brainkb:hasAssertionCategory
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alias: hasAssertionCategory
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range: Categories
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has_assertion_method:
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description: The brainkb:hasAssertionMethod property relates an eco:Assertion
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to an eco:assertion method that differentiates different types of assertions
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techniques used while making an assertion.
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from_schema: https://identifiers.org/brain-bican/assertion-evidence-schema
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slot_uri: brainkb:hasAssertionMethod
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alias: hasAssertionMethod
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range: AssertionMethod
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has_assertion_text:
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description: The brainkb:hasAssertionText property relates an eco:Assertion
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to an xsd:string, providing a textual excerpt of the assertion being made.
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from_schema: https://identifiers.org/brain-bican/assertion-evidence-schema
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slot_uri: brainkb:hasAssertionText
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alias: hasAssertionText
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range: string
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class_uri: sepio:Assertion
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AssertionMethod:
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description: A means by which a statement is made about the entity
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class_uri: eco:0000217
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AssertionSummary:
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description: A summary is a brief statement or description of the main points,
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especially as a conclusion to a work about the assertion.
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from_schema: https://identifiers.org/brain-bican/assertion-evidence-schema
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slots:
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- is_associated_with
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slot_usage:
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is_associated_with:
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description: The brainkb:isAssociatedWith property establishes relationships
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between different entities:it links sepio:Assertion to brainkb:AssertionSummary,
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indicating the association between an assertion and its corresponding summary.
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slot_uri: brainkb:isAssociatedWith
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alias: isAssociatedWith
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range: Assertion
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attributes:
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has_assertion_summary:
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description: The brainkb:hasAssertionSummary property relates a brainkb:AssertionSummary
@@ -199,11 +243,27 @@ classes:
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alias: hasAssertionSummary
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range: string
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class_uri: brainkb:AssertionSummary
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Document:
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description: A collection of information content entities intended to be understood
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together as a whole
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from_schema: https://identifiers.org/brain-bican/assertion-evidence-schema
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class_uri: sepio:Document
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EvidenceLine:
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description: An evidence line represents an independent and meaningful argument
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for or against a particular proposition, that is based on the interpretation
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of one or more pieces of information as evidence.
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from_schema: https://identifiers.org/brain-bican/assertion-evidence-schema
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slots:
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- is_described_by
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slot_usage:
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is_described_by:
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slot_uri: sepio:is_described_by
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range: Document
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class_uri: sepio:0000002
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EvidenceSummary:
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description: A summary is a brief statement or description of the main points,
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especially as a conclusion to a work about the evidence.
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from_schema: https://identifiers.org/brain-bican/assertion-evidence-schema
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attributes:
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has_evidence_summary:
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description: The brainkb:hasEvidenceSummary property relates a brainkb:EvidenceSummary
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alias: hasEvidenceSummary
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range: string
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class_uri: brainkb:EvidenceSummary
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AssertionMethod:
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description: A means by which a statement is made about the entity
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from_schema: https://identifiers.org/brain-bican/assertion-evidence-schema
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class_uri: eco:0000217
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DataAnnotation:
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from_schema: https://identifiers.org/brain-bican/assertion-evidence-schema
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class_uri: brainkb:DataAnnotation
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Evidence:
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from_schema: https://identifiers.org/brain-bican/assertion-evidence-schema
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slots:
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- used_in
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- is_associated_with
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slot_usage:
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used_in: {}
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is_associated_with:
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description: 'The brainkb:isAssociatedWith property establishes relationships
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between different entities: it associates eco:Evidence with brainkb:EvidenceSummary,
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signifying the connection between evidence and its summarized representation.'
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range: EvidenceSummary
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attributes:
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has_evidence_category:
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description: The brainkb:hasEvidenceCategory property relates brainkb:Evidence

‎linkml-schema/source_assertion_evidence/gsheet_output/Classes.tsv‎

Lines changed: 12 additions & 11 deletions
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ç Inheritance: is_a Inheritance: mixin Inheritance: slot usage Subsets Definition
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> class is_a mixins ignore in_subset description class_uri mixin
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> internal_separator: "|" internal_separator: "|"
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Assertion A statement made by a particular agent on a particular occasion that a particular proposition is true, based on the evaluation of one or more lines of evidence. sepio:Assertion
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Document A collection of information content entities intended to be understood together as a whole sepio:Document
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Activity An activity is something that occurs over a period of time and acts upon or with entities; it may include consuming, processing, transforming, modifying, relocating, using, or generating entities. prov:Activity
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Agent An agent is something that bears some form of responsibility for an activity taking place, for the existence of an entity, or for another agent's activity. prov:Agent
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AssertionSummary A summary is a brief statement or description of the main points, especially as a conclusion to a work about the assertion. brainkb:AssertionSummary
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EvidenceSummary A summary is a brief statement or description of the main points, especially as a conclusion to a work about the evidence. brainkb:EvidenceSummary
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AssertionMethod A means by which a statement is made about the entity eco:0000217
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DataAnnotation brainkb:DataAnnotation
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class Inheritance: is_a Inheritance: mixin Subsets Definition
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> class is_a mixins in_subset description class_uri mixin
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> internal_separator: "|" internal_separator: "|"
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Activity An activity is something that occurs over a period of time and acts upon or with entities; it may include consuming, processing, transforming, modifying, relocating, using, or generating entities. prov:Activity
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Agent An agent is something that bears some form of responsibility for an activity taking place, for the existence of an entity, or for another agent's activity. prov:Agent
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Annotation An annotation is a written explanatory or critical description, or other in-context information (e.g., pattern, motif, link), that has been associated with data or other types of information. oa:Annotation
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Assertion A statement made by a particular agent on a particular occasion that a particular proposition is true, based on the evaluation of one or more lines of evidence. sepio:Assertion
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AssertionMethod A means by which a statement is made about the entity eco:0000217
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AssertionSummary A summary is a brief statement or description of the main points, especially as a conclusion to a work about the assertion. brainkb:AssertionSummary
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Document A collection of information content entities intended to be understood together as a whole sepio:Document
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EvidenceLine An evidence line represents an independent and meaningful argument for or against a particular proposition, that is based on the interpretation of one or more pieces of information as evidence. sepio:0000002
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EvidenceSummary A summary is a brief statement or description of the main points, especially as a conclusion to a work about the evidence. brainkb:EvidenceSummary

‎linkml-schema/source_assertion_evidence/gsheet_output/Relations.tsv‎

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Object Predicate (more general) Subject Multivalued ExactlyOneOf (True/False, default=False) Required (True/False) Slot Definition Property Type Characteristics Addition information Suggestions/Comments Suggested/Commented by
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> class slot range slot_uri multivalued ignore required description ignore ignore ignore ignore ignore
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>
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uses Evidence The eco:uses property is the inverse of the eco:used_in property and defines the relationship between eco:Assertion and eco:Evidence, indicating that an assertion relies on the evidence. Object Property Functional inverse of eco:used_in
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used_in Assertion The eco:used_in property establishes a relationship between eco:Evidence and eco:Assertion, indicating that the evidence is utilized to support the corresponding assertion. Object Property Functional inverse of eco:uses
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has_assertion_method AssertionMethod The brainkb:hasAssertionMethod property relates an eco:Assertion to an brainkb:AssertionMethod that differentiates different types of assertions techniques used while making an assertion. Object Property Functional
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Evidence used_in Object Property Functional inverse of eco:uses
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Assertion has_assertion_method The brainkb:hasAssertionMethod property relates an eco:Assertion to an brainkb:AssertionMethod that differentiates different types of assertions techniques used while making an assertion. Object Property Functional
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Agent is_associated_with Activity The brainkb:isAssociatedWith property establishes relationships between different entities: it connects prov:Agent to prov:Activity, reflecting the involvement or connection between an agent and an activity. Object Property
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Assertion is_associated_with AssertionSummary The brainkb:isAssociatedWith property establishes relationships between different entities:it links sepio:Assertion to brainkb:AssertionSummary, indicating the association between an assertion and its corresponding summary. Object Property
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Assertion has_data_annotation DataAnnotation
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Evidence is_associated_with EvidenceSummary The brainkb:isAssociatedWith property establishes relationships between different entities: it associates eco:Evidence with brainkb:EvidenceSummary, signifying the connection between evidence and its summarized representation. Object Property
1+
Object Predicate (more general) Subject Alias Multivalued ExactlyOneOf (True/False, default=False) Required (True/False) Slot Definition Property Type Characteristics Addition information Suggestions/Comments Suggested/Commented by
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> class slot range alias slot_uri multivalued ignore required description ignore ignore ignore ignore ignore
3+
>
4+
uses Evidence The eco:uses property is the inverse of the eco:used_in property and defines the relationship between eco:Assertion and eco:Evidence, indicating that an assertion relies on the evidence. Object Property Functional inverse of eco:used_in
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used_in Assertion The eco:used_in property establishes a relationship between eco:Evidence and eco:Assertion, indicating that the evidence is utilized to support the corresponding assertion. Object Property Functional inverse of eco:uses
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has_assertion_method AssertionMethod The brainkb:hasAssertionMethod property relates an eco:Assertion to an brainkb:AssertionMethod that differentiates different types of assertions techniques used while making an assertion. Object Property Functional
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Agent is_associated_with Activity The brainkb:isAssociatedWith property establishes relationships between different entities: it connects prov:Agent to prov:Activity, reflecting the involvement or connection between an agent and an activity. Object Property
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Assertion has_annotation Annotation sio:hasAnnotation
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Assertion has_assertion_method The brainkb:hasAssertionMethod property relates an eco:Assertion to an brainkb:AssertionMethod that differentiates different types of assertions techniques used while making an assertion. Object Property Functional
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Assertion has_summary AssertionSummary hasSummary brainkb:hasSummary
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Assertion has_evidence_line EvidenceLine sepio:hasEvidenceLine A relationship between an assertion or proposition and an evidence line used in evaluating its validity. Object Property Functional
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Assertion is_expressed_in Document sepio:is_expressed_in
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AssertionSummary is_associated_with Assertion isAssociatedWith brainkb:isAssociatedWith The brainkb:isAssociatedWith property establishes relationships between different entities:it links sepio:Assertion to brainkb:AssertionSummary, indicating the association between an assertion and its corresponding summary. Object Property
14+
Evidence is_associated_with EvidenceSummary The brainkb:isAssociatedWith property establishes relationships between different entities: it associates eco:Evidence with brainkb:EvidenceSummary, signifying the connection between evidence and its summarized representation. Object Property
15+
EvidenceLine is_described_by Document sepio:is_described_by

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