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Merge pull request #78 from puja-trivedi/assertion_evidence_model
[WIP] Assertion evidence model
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‎linkml-schema/assertion_evidence.yaml‎

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name: assertion-evidence-schema
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title: Assertion Evidence Schema
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id: https://identifiers.org/brain-bican/assertion-evidence-schema
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imports:
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- linkml:types
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prefixes:
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linkml: https://w3id.org/linkml/
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bican: https://identifiers.org/brain-bican/vocab/
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spdx: http://spdx.org/rdf/terms#
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schema: http://schema.org/
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brainkb: https://brainkb.org/
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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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default_prefix: brainkb
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default_range: string
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enums:
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AssertionType:
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from_schema: https://identifiers.org/brain-bican/assertion-evidence-schema
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permissible_values:
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Positive: {}
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Negative: {}
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Inconclusive: {}
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Categories:
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from_schema: https://identifiers.org/brain-bican/assertion-evidence-schema
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permissible_values:
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Behavioral: {}
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Biomarker: {}
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DrugTarget: {}
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Genetic: {}
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ClinicalTrial: {}
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Etiologic: {}
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Neuroimaging: {}
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Electrophysiological: {}
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Molecular: {}
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Pharmacological: {}
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Neuropsychological: {}
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Neurogenetic: {}
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Neurochemical: {}
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Neuroanatomical: {}
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Neurodevelopmental: {}
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Neuroinflammatory: {}
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Neuroplasticity: {}
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Neuropathological: {}
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Neurocomputational: {}
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Neuroendocrine: {}
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Neuropharmacogenomic: {}
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Neuroproteomic: {}
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Neurogenomic: {}
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Epigenetic: {}
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Environmental: {}
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Translational: {}
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Therapeutic: {}
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CognitiveNeuroscience: {}
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SignificanceLevel:
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from_schema: https://identifiers.org/brain-bican/assertion-evidence-schema
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permissible_values:
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HighlySignificant:
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description: P value less than 0.01
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Significant:
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description: P value less than 0.05
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MarginallySignificant:
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description: P value less than 0.10
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NotSignificant:
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description: P value greater than or equal to 0.10
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Unknown:
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description: Specifies that the significance level is unknown as the information
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is not present in the study.
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Significance:
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from_schema: https://identifiers.org/brain-bican/assertion-evidence-schema
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permissible_values:
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Clinical: {}
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NonClinical: {}
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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
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and defines the relationship between eco:Assertion and eco:Evidence, indicating
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that an assertion relies on the evidence.
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from_schema: https://identifiers.org/brain-bican/assertion-evidence-schema
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range: Evidence
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used_in:
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description: The eco:used_in property establishes a relationship between eco:Evidence
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and eco:Assertion, indicating that the evidence is utilized to support the corresponding
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assertion.
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from_schema: https://identifiers.org/brain-bican/assertion-evidence-schema
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range: Assertion
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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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from_schema: https://identifiers.org/brain-bican/assertion-evidence-schema
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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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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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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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from_schema: https://identifiers.org/brain-bican/assertion-evidence-schema
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class_uri: sepio:Document
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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
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and xsd:DateTime that allows one to specify the time when the activity ended.
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from_schema: https://identifiers.org/brain-bican/assertion-evidence-schema
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alias: endedAtTime
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range: datetime
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started_at_time:
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description: The prov:startedAtTime establishes the relationship between prov:Activity
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and xsd:DateTime that allows one to specify the time when the activity started.
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from_schema: https://identifiers.org/brain-bican/assertion-evidence-schema
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alias: startedAtTime
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range: datetime
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class_uri: prov:Activity
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Agent:
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description: An agent is something that bears some form of responsibility for
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an activity taking place, for the existence of an entity, or for another agent's
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activity.
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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 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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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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attributes:
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has_assertion_summary:
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description: The brainkb:hasAssertionSummary property relates a brainkb:AssertionSummary
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to an xsd:string, providing a concise overview that differentiates various
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assertions. This summary encapsulates the core content of the assertion,
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allowing for easy identification and understanding of its essence.
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from_schema: https://identifiers.org/brain-bican/assertion-evidence-schema
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slot_uri: brainkb:hasAssertionSummary
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alias: hasAssertionSummary
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range: string
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class_uri: brainkb:AssertionSummary
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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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to an xsd:string, providing a concise overview that differentiates various
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evidence. This summary encapsulates the core content of the evidence, allowing
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for easy identification and understanding of its essence.
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from_schema: https://identifiers.org/brain-bican/assertion-evidence-schema
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slot_uri: brainkb:hasEvidenceSummary
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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
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and brainkb:Categories, specifying the classification or category that the
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evidence belongs to.
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from_schema: https://identifiers.org/brain-bican/assertion-evidence-schema
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slot_uri: brainkb:hasEvidenceCategory
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alias: hasEvidenceCategory
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range: Categories
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has_evidence_text:
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description: The brainkb:hasEvidenceText property relates an eco:Evidence
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to an xsd:string, providing a textual excerpt of the evidence supporting
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the assertion.
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from_schema: https://identifiers.org/brain-bican/assertion-evidence-schema
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slot_uri: brainkb:hasEvidenceText
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alias: hasEvidenceText
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range: string

‎linkml-schema/source_assertion_evidence/gsheet.yaml‎

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gsheet_id: "1UpjNNJz9o1TXpPS245tbPsVbIx_p5_m2f54KoIwGF8g"
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sheets:
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- name: "Classes"
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gid: "1224768617"
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- name: "Relations"
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gid: "1748292296"
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- name: "Slots"
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gid: "581500779"
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- name: "Prefixes"
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gid: "403981074"
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- name: "ValueSets"
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gid: "743520255"

‎linkml-schema/source_assertion_evidence/gsheet_output/Classes.tsv‎

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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

‎linkml-schema/source_assertion_evidence/gsheet_output/Prefixes.tsv‎

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prefix uri default schema imports title description id
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brainkb assertion-evidence-schema Assertion Evidence Schema https://identifiers.org/brain-bican/assertion-evidence-schema
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> prefix prefix_reference default_prefix schema imports title description id
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linkml https://w3id.org/linkml/
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bican https://identifiers.org/brain-bican/vocab/
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spdx http://spdx.org/rdf/terms#
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schema http://schema.org/
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brainkb https://brainkb.org/
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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_

‎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

‎linkml-schema/source_assertion_evidence/gsheet_output/Slots.tsv‎

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LinkML Slot or Attribute Name BICAN UUID SubGroup/LinkML Class Name Aliases Definition Nullable Multivalued Permissible Values Data Type Data Examples Min Value Max Value Unit Statistical Type Subsets Notes
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> alias attribute slot_uri class ignore description ignore multivalued ignore range ignore ignore ignore ignore ignore in_subset ignore
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> internal_separator: "|"
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hasAssertionCategory has_assertion_category brainkb:hasAssertionCategory Assertion The brainkb:hasAssertionCategory property relates brainkb:Evidence and brainkb:Categories, specifying the classification or category that the assertion belongs to. FALSE Categories Object Property
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hasEvidenceCategory has_evidence_category brainkb:hasEvidenceCategory Evidence The brainkb:hasEvidenceCategory property relates brainkb:Evidence and brainkb:Categories, specifying the classification or category that the evidence belongs to. FALSE Categories Object Property
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hasEvidenceText has_evidence_text brainkb:hasEvidenceText Evidence The brainkb:hasEvidenceText property relates an eco:Evidence to an xsd:string, providing a textual excerpt of the evidence supporting the assertion. FALSE string Data Property
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hasAssertionText has_assertion_text brainkb:hasAssertionText Assertion The brainkb:hasAssertionText property relates an eco:Assertion to an xsd:string, providing a textual excerpt of the assertion being made. FALSE string Data Property
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hasAssertionMethod has_assertion_method brainkb:hasAssertionMethod Assertion The brainkb:hasAssertionMethod property relates an eco:Assertion to an eco:assertion method that differentiates different types of assertions techniques used while making an assertion. FALSE AssertionMethod Object Property
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hasAssertionSummary has_assertion_summary brainkb:hasAssertionSummary AssertionSummary The brainkb:hasAssertionSummary property relates a brainkb:AssertionSummary to an xsd:string, providing a concise overview that differentiates various assertions. This summary encapsulates the core content of the assertion, allowing for easy identification and understanding of its essence. FALSE string Data Property
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hasEvidenceSummary has_evidence_summary brainkb:hasEvidenceSummary EvidenceSummary The brainkb:hasEvidenceSummary property relates a brainkb:EvidenceSummary to an xsd:string, providing a concise overview that differentiates various evidence. This summary encapsulates the core content of the evidence, allowing for easy identification and understanding of its essence. FALSE string Data Property
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endedAtTime ended_at_time Activity The prov:endedAtTime establishes the relationship between prov:Activity and xsd:DateTime that allows one to specify the time when the activity ended. FALSE datetime Data Property
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startedAtTime started_at_time Activity The prov:startedAtTime establishes the relationship between prov:Activity and xsd:DateTime that allows one to specify the time when the activity started. FALSE datetime Data Property

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