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Generate new version of the linkml model for assertion_evidence
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puja-trivedi authored Dec 10, 2024
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186 changes: 117 additions & 69 deletions linkml-schema/assertion_evidence.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -12,6 +12,7 @@ prefixes:
prov: http://www.w3.org/ns/prov#
eco: http://purl.obolibrary.org/obo/ECO_
sepio: http://purl.obolibrary.org/obo/SEPIO_
oa: http://www.w3.org/ns/oa#
default_prefix: brainkb
default_range: string
enums:
Expand Down Expand Up @@ -71,6 +72,11 @@ enums:
permissible_values:
Clinical: {}
NonClinical: {}
AssertionMethod:
from_schema: https://identifiers.org/brain-bican/assertion-evidence-schema
permissible_values:
AutomaticAssertion: {}
ManualAssertion: {}
slots:
uses:
description: The eco:uses property is the inverse of the eco:used_in property
Expand All @@ -92,68 +98,22 @@ slots:
range: AssertionMethod
is_associated_with:
from_schema: https://identifiers.org/brain-bican/assertion-evidence-schema
has_data_annotation:
has_annotation:
from_schema: https://identifiers.org/brain-bican/assertion-evidence-schema
classes:
Assertion:
description: 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.
has_summary:
from_schema: https://identifiers.org/brain-bican/assertion-evidence-schema
slots:
- has_assertion_method
- is_associated_with
- has_data_annotation
slot_usage:
has_assertion_method:
description: The brainkb:hasAssertionMethod property relates an eco:Assertion
to an brainkb:AssertionMethod that differentiates different types of assertions
techniques used while making an assertion.
is_associated_with:
description: 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.
range: AssertionSummary
has_data_annotation:
range: DataAnnotation

attributes:
has_assertion_category:
description: The brainkb:hasAssertionCategory property relates brainkb:Evidence
and brainkb:Categories, specifying the classification or category that the
assertion belongs to.
from_schema: https://identifiers.org/brain-bican/assertion-evidence-schema
slot_uri: brainkb:hasAssertionCategory
alias: hasAssertionCategory
range: Categories
has_assertion_text:
description: The brainkb:hasAssertionText property relates an eco:Assertion
to an xsd:string, providing a textual excerpt of the assertion being made.
from_schema: https://identifiers.org/brain-bican/assertion-evidence-schema
slot_uri: brainkb:hasAssertionText
alias: hasAssertionText
range: string
has_assertion_method:
description: 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.
from_schema: https://identifiers.org/brain-bican/assertion-evidence-schema
slot_uri: brainkb:hasAssertionMethod
alias: hasAssertionMethod
range: AssertionMethod
class_uri: sepio:Assertion
Document:
description: A collection of information content entities intended to be understood
together as a whole
has_evidence_line:
from_schema: https://identifiers.org/brain-bican/assertion-evidence-schema

class_uri: sepio:Document
is_expressed_in:
from_schema: https://identifiers.org/brain-bican/assertion-evidence-schema
is_described_by:
from_schema: https://identifiers.org/brain-bican/assertion-evidence-schema
classes:
Activity:
description: 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.
from_schema: https://identifiers.org/brain-bican/assertion-evidence-schema

attributes:
ended_at_time:
description: The prov:endedAtTime establishes the relationship between prov:Activity
Expand Down Expand Up @@ -181,13 +141,97 @@ classes:
between different entities: it connects prov:Agent to prov:Activity, reflecting
the involvement or connection between an agent and an activity.'
range: Activity

class_uri: prov:Agent
Annotation:
description: 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.
from_schema: https://identifiers.org/brain-bican/assertion-evidence-schema
attributes:
cell_annotation:
from_schema: https://identifiers.org/brain-bican/assertion-evidence-schema
slot_uri: brainkb:cellAnnotation
alias: cellAnnotation
range: string
description:
from_schema: https://identifiers.org/brain-bican/assertion-evidence-schema
slot_uri: brainkb:description
alias: description
range: string
class_uri: oa:Annotation
Assertion:
description: 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.
from_schema: https://identifiers.org/brain-bican/assertion-evidence-schema
slots:
- has_annotation
- has_assertion_method
- has_summary
- has_evidence_line
- is_expressed_in
slot_usage:
has_annotation:
slot_uri: sio:hasAnnotation
range: Annotation
has_assertion_method:
description: The brainkb:hasAssertionMethod property relates an eco:Assertion
to an brainkb:AssertionMethod that differentiates different types of assertions
techniques used while making an assertion.
has_summary:
slot_uri: brainkb:hasSummary
alias: hasSummary
range: AssertionSummary
has_evidence_line:
description: A relationship between an assertion or proposition and an evidence
line used in evaluating its validity.
slot_uri: sepio:hasEvidenceLine
range: EvidenceLine
is_expressed_in:
slot_uri: sepio:is_expressed_in
range: Document
attributes:
has_assertion_category:
description: The brainkb:hasAssertionCategory property relates brainkb:Evidence
and brainkb:Categories, specifying the classification or category that the
assertion belongs to.
from_schema: https://identifiers.org/brain-bican/assertion-evidence-schema
slot_uri: brainkb:hasAssertionCategory
alias: hasAssertionCategory
range: Categories
has_assertion_method:
description: 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.
from_schema: https://identifiers.org/brain-bican/assertion-evidence-schema
slot_uri: brainkb:hasAssertionMethod
alias: hasAssertionMethod
range: AssertionMethod
has_assertion_text:
description: The brainkb:hasAssertionText property relates an eco:Assertion
to an xsd:string, providing a textual excerpt of the assertion being made.
from_schema: https://identifiers.org/brain-bican/assertion-evidence-schema
slot_uri: brainkb:hasAssertionText
alias: hasAssertionText
range: string
class_uri: sepio:Assertion
AssertionMethod:
description: A means by which a statement is made about the entity
class_uri: eco:0000217
AssertionSummary:
description: A summary is a brief statement or description of the main points,
especially as a conclusion to a work about the assertion.
from_schema: https://identifiers.org/brain-bican/assertion-evidence-schema

slots:
- is_associated_with
slot_usage:
is_associated_with:
description: 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.
slot_uri: brainkb:isAssociatedWith
alias: isAssociatedWith
range: Assertion
attributes:
has_assertion_summary:
description: The brainkb:hasAssertionSummary property relates a brainkb:AssertionSummary
Expand All @@ -199,11 +243,27 @@ classes:
alias: hasAssertionSummary
range: string
class_uri: brainkb:AssertionSummary
Document:
description: A collection of information content entities intended to be understood
together as a whole
from_schema: https://identifiers.org/brain-bican/assertion-evidence-schema
class_uri: sepio:Document
EvidenceLine:
description: 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.
from_schema: https://identifiers.org/brain-bican/assertion-evidence-schema
slots:
- is_described_by
slot_usage:
is_described_by:
slot_uri: sepio:is_described_by
range: Document
class_uri: sepio:0000002
EvidenceSummary:
description: A summary is a brief statement or description of the main points,
especially as a conclusion to a work about the evidence.
from_schema: https://identifiers.org/brain-bican/assertion-evidence-schema

attributes:
has_evidence_summary:
description: The brainkb:hasEvidenceSummary property relates a brainkb:EvidenceSummary
Expand All @@ -215,28 +275,16 @@ classes:
alias: hasEvidenceSummary
range: string
class_uri: brainkb:EvidenceSummary
AssertionMethod:
description: A means by which a statement is made about the entity
from_schema: https://identifiers.org/brain-bican/assertion-evidence-schema

class_uri: eco:0000217
DataAnnotation:
from_schema: https://identifiers.org/brain-bican/assertion-evidence-schema

class_uri: brainkb:DataAnnotation
Evidence:
from_schema: https://identifiers.org/brain-bican/assertion-evidence-schema
slots:
- used_in
- is_associated_with
slot_usage:
used_in: {}
is_associated_with:
description: '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.'
range: EvidenceSummary

attributes:
has_evidence_category:
description: The brainkb:hasEvidenceCategory property relates brainkb:Evidence
Expand Down
23 changes: 12 additions & 11 deletions linkml-schema/source_assertion_evidence/gsheet_output/Classes.tsv
Original file line number Diff line number Diff line change
@@ -1,11 +1,12 @@
ç Inheritance: is_a Inheritance: mixin Inheritance: slot usage Subsets Definition
> class is_a mixins ignore in_subset description class_uri mixin
> internal_separator: "|" internal_separator: "|"
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
Document A collection of information content entities intended to be understood together as a whole sepio:Document
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
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
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
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
AssertionMethod A means by which a statement is made about the entity eco:0000217
DataAnnotation brainkb:DataAnnotation
class Inheritance: is_a Inheritance: mixin Subsets Definition
> class is_a mixins in_subset description class_uri mixin
> internal_separator: "|" internal_separator: "|"
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
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
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
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
AssertionMethod A means by which a statement is made about the entity eco:0000217
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
Document A collection of information content entities intended to be understood together as a whole sepio:Document
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
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
27 changes: 15 additions & 12 deletions linkml-schema/source_assertion_evidence/gsheet_output/Relations.tsv
Original file line number Diff line number Diff line change
@@ -1,12 +1,15 @@
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
> class slot range slot_uri multivalued ignore required description ignore ignore ignore ignore ignore
>
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
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
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
Evidence used_in Object Property Functional inverse of eco:uses
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
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
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
Assertion has_data_annotation DataAnnotation
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
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
> class slot range alias slot_uri multivalued ignore required description ignore ignore ignore ignore ignore
>
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
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
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
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
Assertion has_annotation Annotation sio:hasAnnotation
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
Assertion has_summary AssertionSummary hasSummary brainkb:hasSummary
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
Assertion is_expressed_in Document sepio:is_expressed_in
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
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
EvidenceLine is_described_by Document sepio:is_described_by
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