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Auto PR: assertion_evidence.yaml generated from google spreadsheets using schemasheets #128

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06ddac4
Generate new version of the linkml model for assertion_evidence
puja-trivedi Dec 18, 2024
03bc9ec
generate another formats for assertion_evidence model
Dec 18, 2024
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70 changes: 51 additions & 19 deletions erdiagram-autogen/assertion_evidence.md
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@@ -1,42 +1,74 @@
```mermaid
erDiagram
Activity {
datetime ended_at_time
datetime started_at_time
}
Agent {

}
Annotation {

}
Assertion {
string is_expressed_in
Categories has_assertion_category
string has_assertion_text
AssertionType has_assertion_type
SignificanceLevel significance_level
Significance significance_type
}
CellAnnotation {

}
Document {
uri identifier
}
EvidenceLine {
string description
Categories has_evidence_category
EvidenceType has_evidence_type
}
Group {

}
Activity {
datetime ended_at_time
datetime started_at_time
Identifier {

}
Agent {
OrcidIdentifier {

}
AssertionSummary {
string has_assertion_summary
Organization {

}
EvidenceSummary {
string has_evidence_summary
Person {
ContributorType contributor_type
}
AssertionMethod {
PersonIdentifier {

}
DataAnnotation {
Platform {

}
Evidence {
Categories has_evidence_category
string has_evidence_text
SoftwareAgent {

}
Source {

}

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 Agent : "has_contributer"
Assertion ||--|o EvidenceLine : "has_evidence_line"
EvidenceLine ||--|o Agent : "has_contributer"
EvidenceLine ||--|o Activity : "output_of"
EvidenceLine ||--|o Document : "has_supporting_reference"
Group ||--|o Identifier : "has_identifier"
Organization ||--|o Identifier : "has_identifier"
Person ||--|o Identifier : "has_identifier"
SoftwareAgent ||--|o Identifier : "has_identifier"

```

226 changes: 173 additions & 53 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 @@ -22,14 +25,19 @@
"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.",
Expand All @@ -38,41 +46,42 @@
"$ref": "#/$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_annotation": {
"$ref": "#/$defs/Annotation"
},
"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_text": {
"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_assertion_type": {
"$ref": "#/$defs/AssertionType"
},
"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."
}
},
"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.",
"has_contributer": {
"$ref": "#/$defs/Agent"
},
"has_evidence_line": {
"$ref": "#/$defs/EvidenceLine",
"description": "A relationship between an assertion or proposition and an evidence line used in evaluating its validity."
},
"is_expressed_in": {
"anyOf": [
{
"$ref": "#/$defs/Document"
},
{
"$ref": "#/$defs/Platform"
}
],
"type": "string"
},
"significance_level": {
"$ref": "#/$defs/SignificanceLevel"
},
"significance_type": {
"$ref": "#/$defs/Significance"
}
},
"title": "AssertionSummary",
"title": "Assertion",
"type": "object"
},
"AssertionType": {
Expand Down Expand Up @@ -120,52 +129,146 @@
"title": "Categories",
"type": "string"
},
"DataAnnotation": {
"CellAnnotation": {
"additionalProperties": false,
"description": "",
"title": "DataAnnotation",
"title": "CellAnnotation",
"type": "object"
},
"ContributorType": {
"description": "",
"enum": [
"datacite:ContactPerson",
"datacite:DataCollector",
"datacite:DataCurator",
"datacite:DataManager",
"datacite:Distributor",
"datacite:Editor",
"datacite:HostingInstitution",
"datacite:Producer",
"datacite:ProjectLeader",
"datacite:ProjectManager",
"datacite:ProjectMember",
"datacite:RegistrationAgency",
"datacite:RegistrationAuthority",
"datacite:RelatedPerson",
"datacite:Researcher",
"datacite:ResearchGroup",
"datacite:RightsHolder",
"datacite:Sponsor",
"datacite:Supervisor",
"datacite:WorkPackageLeader"
],
"title": "ContributorType",
"type": "string"
},
"Document": {
"additionalProperties": false,
"description": "A collection of information content entities intended to be understood together as a whole",
"properties": {
"identifier": {
"type": "string"
}
},
"title": "Document",
"type": "object"
},
"Evidence": {
"EvidenceLine": {
"additionalProperties": false,
"description": "",
"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": {
"description": {
"type": "string"
},
"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."
"$ref": "#/$defs/Categories"
},
"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"
"hasEvidenceType": {
"$ref": "#/$defs/EvidenceType"
},
"has_contributer": {
"$ref": "#/$defs/Agent",
"description": "A relation between an information content entity and an agent who made a contribution to its information content, or to its subsequent modification or assessment."
},
"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."
"has_supporting_reference": {
"$ref": "#/$defs/Document",
"description": "A relation that holds between an evidence line and a citable document from which information supporting the evidence line was obtained (i.e. a \"supporting reference\")."
},
"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."
"output_of": {
"$ref": "#/$defs/Activity"
}
},
"title": "Evidence",
"title": "EvidenceLine",
"type": "object"
},
"EvidenceSummary": {
"EvidenceType": {
"description": "",
"enum": [
"SupportingEvidence",
"DisputingEvidence",
"InconclusiveEvidence"
],
"title": "EvidenceType",
"type": "string"
},
"Group": {
"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": "",
"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.",
"type": "string"
"has_identifier": {
"$ref": "#/$defs/Identifier"
}
},
"title": "EvidenceSummary",
"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": {
"contributorType": {
"$ref": "#/$defs/ContributorType"
},
"has_identifier": {
"$ref": "#/$defs/Identifier"
}
},
"title": "Person",
"type": "object"
},
"PersonIdentifier": {
"additionalProperties": false,
"description": "",
"title": "PersonIdentifier",
"type": "object"
},
"Platform": {
"additionalProperties": false,
"description": "",
"title": "Platform",
"type": "object"
},
"Significance": {
Expand All @@ -188,6 +291,23 @@
],
"title": "SignificanceLevel",
"type": "string"
},
"SoftwareAgent": {
"additionalProperties": false,
"description": "",
"properties": {
"has_identifier": {
"$ref": "#/$defs/Identifier"
}
},
"title": "SoftwareAgent",
"type": "object"
},
"Source": {
"additionalProperties": false,
"description": "",
"title": "Source",
"type": "object"
}
},
"$id": "https://identifiers.org/brain-bican/assertion-evidence-schema",
Expand Down
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