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Merge pull request #130 from brain-bican/autogenerated-yaml-202412200…
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Auto PR: assertion_evidence.yaml generated from google spreadsheets using schemasheets
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@djarecka
djarecka authored Jan 6, 2025
2 parents 514a269 + 8073cc6 commit 87f4b32
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69 changes: 49 additions & 20 deletions erdiagram-autogen/assertion_evidence.md
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@@ -1,42 +1,71 @@
```mermaid
erDiagram
Activity {
datetime ended_at_time
datetime started_at_time
}
Agent {
}
Annotation {
}
Assertion {
Categories has_assertion_category
string has_assertion_text
string has_assertion_description
string has_assertion_summary
}
CellAnnotation {
}
Document {
uri identifier
}
EvidenceItem {
}
Activity {
datetime ended_at_time
datetime started_at_time
EvidenceLine {
EvidenceDirection evidence_direction
EvidenceStrength evidence_line_strength
Categories has_evidence_category
string has_evidenceline_description
}
Agent {
Group {
}
AssertionSummary {
string has_assertion_summary
Identifier {
}
EvidenceSummary {
string has_evidence_summary
OrcidIdentifier {
}
AssertionMethod {
Organization {
}
DataAnnotation {
Person {
}
Evidence {
Categories has_evidence_category
string has_evidence_text
PersonIdentifier {
}
SoftwareAgent {
}
Assertion ||--|o AssertionMethod : "has_assertion_method"
Assertion ||--|o AssertionSummary : "is_associated_with"
Assertion ||--|o DataAnnotation : "has_data_annotation"
Agent ||--|o Activity : "is_associated_with"
Evidence ||--|o Assertion : "used_in"
Evidence ||--|o EvidenceSummary : "is_associated_with"
Activity ||--|o Agent : "was_associate_with"
Agent ||--|o Identifier : "has_identifier"
Assertion ||--|o Annotation : "has_annotation"
Assertion ||--|o Activity : "was_generated_by"
Assertion ||--|o EvidenceLine : "has_evidence_line"
Document ||--|o Document : "reference"
EvidenceItem ||--|o Document : "reference"
EvidenceLine ||--|o EvidenceItem : "has_evidence_item"
EvidenceLine ||--|o Activity : "was_generated_by"
Group ||--|o Identifier : "has_identifier"
Organization ||--|o Identifier : "has_identifier"
Person ||--|o Organization : "member"
Person ||--|o Identifier : "has_identifier"
SoftwareAgent ||--|o Identifier : "has_identifier"
```

214 changes: 137 additions & 77 deletions json-schema-autogen/assertion_evidence.json
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Expand Up @@ -13,6 +13,9 @@
"description": "The prov:startedAtTime establishes the relationship between prov:Activity and xsd:DateTime that allows one to specify the time when the activity started.",
"format": "date-time",
"type": "string"
},
"was_associate_with": {
"$ref": "#/$defs/Agent"
}
},
"title": "Activity",
Expand All @@ -22,69 +25,48 @@
"additionalProperties": false,
"description": "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.",
"properties": {
"is_associated_with": {
"$ref": "#/$defs/Activity",
"description": "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."
"has_identifier": {
"$ref": "#/$defs/Identifier"
}
},
"title": "Agent",
"type": "object"
},
"Annotation": {
"additionalProperties": false,
"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.",
"title": "Annotation",
"type": "object"
},
"Assertion": {
"additionalProperties": false,
"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.",
"properties": {
"hasAssertionCategory": {
"has_annotation": {
"$ref": "#/$defs/Annotation"
},
"has_assertion_category": {
"$ref": "#/$defs/Categories",
"description": "The brainkb:hasAssertionCategory property relates brainkb:Evidence and brainkb:Categories, specifying the classification or category that the assertion belongs to."
},
"hasAssertionMethod": {
"$ref": "#/$defs/AssertionMethod",
"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_assertion_description": {
"type": "string"
},
"hasAssertionText": {
"description": "The brainkb:hasAssertionText property relates an eco:Assertion to an xsd:string, providing a textual excerpt of the assertion being made.",
"has_assertion_summary": {
"description": "The brainkb:has_assertion_text property relates an eco:Assertion to an xsd:string, providing a textual excerpt of the assertion being made.",
"type": "string"
},
"has_data_annotation": {
"$ref": "#/$defs/DataAnnotation"
"has_evidence_line": {
"$ref": "#/$defs/EvidenceLine",
"description": "A relationship between an assertion or proposition and an evidence line used in evaluating its validity."
},
"is_associated_with": {
"$ref": "#/$defs/AssertionSummary",
"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."
"was_generated_by": {
"$ref": "#/$defs/Activity"
}
},
"title": "Assertion",
"type": "object"
},
"AssertionMethod": {
"additionalProperties": false,
"description": "A means by which a statement is made about the entity",
"title": "AssertionMethod",
"type": "object"
},
"AssertionSummary": {
"additionalProperties": false,
"description": "A summary is a brief statement or description of the main points, especially as a conclusion to a work about the assertion.",
"properties": {
"hasAssertionSummary": {
"description": "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.",
"type": "string"
}
},
"title": "AssertionSummary",
"type": "object"
},
"AssertionType": {
"description": "",
"enum": [
"Positive",
"Negative",
"Inconclusive"
],
"title": "AssertionType",
"type": "string"
},
"Categories": {
"description": "",
"enum": [
Expand Down Expand Up @@ -120,64 +102,77 @@
"title": "Categories",
"type": "string"
},
"DataAnnotation": {
"CellAnnotation": {
"additionalProperties": false,
"description": "",
"title": "DataAnnotation",
"title": "CellAnnotation",
"type": "object"
},
"Document": {
"additionalProperties": false,
"description": "A collection of information content entities intended to be understood together as a whole",
"properties": {
"identifier": {
"type": "string"
},
"reference": {
"$ref": "#/$defs/Document"
}
},
"title": "Document",
"type": "object"
},
"Evidence": {
"EvidenceDirection": {
"description": "",
"enum": [
"supporting",
"disputing",
"inconclusive"
],
"title": "EvidenceDirection",
"type": "string"
},
"EvidenceItem": {
"additionalProperties": false,
"description": "",
"properties": {
"hasEvidenceCategory": {
"$ref": "#/$defs/Categories",
"description": "The brainkb:hasEvidenceCategory property relates brainkb:Evidence and brainkb:Categories, specifying the classification or category that the evidence belongs to."
},
"hasEvidenceText": {
"description": "The brainkb:hasEvidenceText property relates an eco:Evidence to an xsd:string, providing a textual excerpt of the evidence supporting the assertion.",
"type": "string"
},
"is_associated_with": {
"$ref": "#/$defs/EvidenceSummary",
"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."
},
"used_in": {
"$ref": "#/$defs/Assertion",
"description": "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."
"reference": {
"$ref": "#/$defs/Document"
}
},
"title": "Evidence",
"title": "EvidenceItem",
"type": "object"
},
"EvidenceSummary": {
"EvidenceLine": {
"additionalProperties": false,
"description": "A summary is a brief statement or description of the main points, especially as a conclusion to a work about the evidence.",
"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.",
"properties": {
"hasEvidenceSummary": {
"description": "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.",
"evidence_direction": {
"$ref": "#/$defs/EvidenceDirection",
"description": "A relation indicating whether an evidence line supports or disputes a target proposition (or represents inconclusive evidence that is not sufficient for either)."
},
"evidence_line_strength": {
"$ref": "#/$defs/EvidenceStrength",
"description": "A relation describing the degree of support provided by an evidence line for a target assertion or proposition."
},
"has_evidence_category": {
"$ref": "#/$defs/Categories"
},
"has_evidence_item": {
"$ref": "#/$defs/EvidenceItem",
"description": "A relation holding between an evidence line and an individual information entity that contributes to the argument it represents."
},
"has_evidenceline_description": {
"type": "string"
},
"was_generated_by": {
"$ref": "#/$defs/Activity"
}
},
"title": "EvidenceSummary",
"title": "EvidenceLine",
"type": "object"
},
"Significance": {
"description": "",
"enum": [
"Clinical",
"NonClinical"
],
"title": "Significance",
"type": "string"
},
"SignificanceLevel": {
"EvidenceStrength": {
"description": "",
"enum": [
"HighlySignificant",
Expand All @@ -186,8 +181,73 @@
"NotSignificant",
"Unknown"
],
"title": "SignificanceLevel",
"title": "EvidenceStrength",
"type": "string"
},
"Group": {
"additionalProperties": false,
"description": "",
"properties": {
"has_identifier": {
"$ref": "#/$defs/Identifier"
}
},
"title": "Group",
"type": "object"
},
"Identifier": {
"additionalProperties": false,
"description": "",
"title": "Identifier",
"type": "object"
},
"OrcidIdentifier": {
"additionalProperties": false,
"description": "",
"title": "OrcidIdentifier",
"type": "object"
},
"Organization": {
"additionalProperties": false,
"description": "",
"properties": {
"has_identifier": {
"$ref": "#/$defs/Identifier"
}
},
"title": "Organization",
"type": "object"
},
"Person": {
"additionalProperties": false,
"description": "",
"properties": {
"has_identifier": {
"$ref": "#/$defs/Identifier"
},
"member": {
"$ref": "#/$defs/Organization"
}
},
"title": "Person",
"type": "object"
},
"PersonIdentifier": {
"additionalProperties": false,
"description": "",
"title": "PersonIdentifier",
"type": "object"
},
"SoftwareAgent": {
"additionalProperties": false,
"description": "",
"properties": {
"has_identifier": {
"$ref": "#/$defs/Identifier"
}
},
"title": "SoftwareAgent",
"type": "object"
}
},
"$id": "https://identifiers.org/brain-bican/assertion-evidence-schema",
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