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One-dimensionalization of data models #613

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merged 7 commits into from
Oct 15, 2024
Merged

One-dimensionalization of data models #613

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9731b30
One-dimensionalization of data models
LzLang Sep 5, 2024
1050824
reformatted to 4 space indent
Sep 6, 2024
20b77c7
added back missing 'description' property
Sep 6, 2024
f9e7b87
corrected case and spelling
Sep 6, 2024
ac35259
corrected TraitDataType id
Sep 13, 2024
25d8fbe
Changed the models accordingly to the review
LzLang Sep 19, 2024
22a9de9
Changed schema according to the review
LzLang Oct 9, 2024
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36 changes: 35 additions & 1 deletion Specification/BrAPI-Schema/BrAPI-Common/GeoJSON.json
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Expand Up @@ -5,6 +5,13 @@
"type": "object",
"description": "One geometry as defined by GeoJSON (RFC 7946). All coordinates are decimal values on the WGS84 geographic coordinate reference system.\n\nCopied from RFC 7946 Section 3.1.1\n\nA position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or\neasting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element.",
"properties": {
"geometryDbId": {
"description": "Unique identifier for the geometry",
"type": [
"null",
"string"
]
},
"geometry": {
"description": "A geometry as defined by GeoJSON (RFC 7946). In this context, only Point or Polygon geometry are allowed.",
"$ref": "GeoJSONGeometry.json#/$defs/GeoJSONGeometry"
Expand All @@ -14,8 +21,35 @@
"default": "Feature",
"example": "Feature",
"description": "The literal string \"Feature\""
},
"image": {
"description": "Geometry associated with an image",
"$ref": "../BrAPI-Phenotyping/Image.json#/$defs/Image",
"relationshipType": "many-to-one",
"referencedAttribute": "imageLocation"
},
"observation": {
"description": "Geometry associated with an image",
"$ref": "../BrAPI-Phenotyping/Observation.json#/$defs/Observation",
"relationshipType": "many-to-one",
"referencedAttribute": "geoCoordinates"
},
"observationUnit": {
"description": "Geometry associated with an image",
"$ref": "../BrAPI-Phenotyping/ObservationUnit.json#/$defs/ObservationUnitPosition",
"relationshipType": "many-to-one",
"referencedAttribute": "geoCoordinates"
},
"germplasmOrigin": {
"description": "Geometry associated with an image",
"$ref": "../BrAPI-Germplasm/Germplasm.json#/$defs/GermplasmOrigin",
"relationshipType": "many-to-one",
"referencedAttribute": "coordinates"
}
}
},
"required": [
"geometryDbId"
]
}
},
"$id": "https://brapi.org/Specification/BrAPI-Schema/BrAPI-Common/GeoJSON.json",
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44 changes: 44 additions & 0 deletions Specification/BrAPI-Schema/BrAPI-Common/SourceGermplasm.json
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@@ -0,0 +1,44 @@
{
"$defs": {
"SourceGermplasm": {
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For this link I would propose to drop SourceGermplasm directly. So in germplasm you would have in Reference and Reference Set

            "sourceGermplasm": {
                "description": "All known corresponding Germplasm",
                "relationshipType": "many-to-many",
                "referencedAttribute": "reference",
                "items": {
                    "$ref": "../BrAPI-Germplasm/Germplasm.json#/$defs/Germplasm",
                },
                "title": "SourceGermplasm",
                "type": [
                    "null",
                    "array"
                ]

Then you could add the back links in Germplasm

"properties": {
"germplasmDbId": {
"description": "The ID which uniquely identifies a `Germplasm` within the given database server",
"type": [
"null",
"string"
]
},
"germplasmName": {
"description": "The human readable name of a `Germplasm`",
"type": [
"null",
"string"
]
},
"reference": {
"description": "Germplasm associated with a reference",
"$ref": "../BrAPI-Genotyping/Reference.json#/$defs/Reference",
"relationshipType": "many-to-one",
"referencedAttribute": "sourceGermplasm"
},
"referenceSet": {
"description": "Germplasm associated with a reference",
"$ref": "../BrAPI-Genotyping/ReferenceSet.json#/$defs/ReferenceSet",
"relationshipType": "many-to-one",
"referencedAttribute": "sourceGermplasm"
}
},
"required": [
"germplasmDbId"
],
"title": "sourceGermplasm",
"type": "object",
"brapi-metadata": {
"primaryModel": false
}
}
},
"$id": "https://brapi.org/Specification/BrAPI-Schema/BrAPI-Common/SourceGermplasm.json",
"$schema": "http://json-schema.org/draft/2020-12/schema"
}
51 changes: 51 additions & 0 deletions Specification/BrAPI-Schema/BrAPI-Common/Species.json
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@@ -0,0 +1,51 @@
{
"$defs": {
"Species": {
"properties": {
"specieDbId": {
"description": "An ontology term describing an attribute.",
"type": [
"null",
"string"
]
},
"term": {
"description": "Ontology term - the label of the ontology term the termId is pointing to.",
"type": [
"null",
"string"
]
},
"termURI": {
"description": "Ontology term identifier - the CURIE for an ontology term. It differs from the standard GA4GH schema's :ref:`id ` in that it is a CURIE pointing to an information resource outside of the scope of the schema or its resource implementation.",
"type": [
"null",
"string"
]
},
"reference": {
"description": "Species associated with a reference",
"$ref": "../BrAPI-Genotyping/Reference.json#/$defs/Reference",
"relationshipType": "many-to-one",
"referencedAttribute": "species"
},
"referenceSet": {
"description": "Species associated with a referenceSet",
"$ref": "../BrAPI-Genotyping/ReferenceSet.json#/$defs/ReferenceSet",
"relationshipType": "many-to-one",
"referencedAttribute": "species"
}
},
"required": [
"specieDbId"
],
"title": "OntologyTerm",
"type": "object",
"brapi-metadata": {
"primaryModel": false
}
}
},
"$id": "https://brapi.org/Specification/BrAPI-Schema/BrAPI-Common/Species.json",
"$schema": "http://json-schema.org/draft/2020-12/schema"
}
14 changes: 12 additions & 2 deletions Specification/BrAPI-Schema/BrAPI-Common/Variable.json
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Expand Up @@ -4,7 +4,15 @@
"properties": {
"additionalInfo": {
"description": "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification.",
"$ref": "../BrAPI-Common/AdditionalInfo.json#/$defs/AdditionalInfo"
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This changes the model, from a single to an array of AdditionalInfo, can this be put in v2.2? See in same changes in other entities.

"relationshipType": "one-to-many",
"items": {
"$ref": "../BrAPI-Common/AdditionalInfo.json#/$defs/AdditionalInfo",
"description": "AdditionalInfo"
},
"type": [
"null",
"array"
]
},
"commonCropName": {
"description": "Crop name (examples: \"Maize\", \"Wheat\")",
Expand Down Expand Up @@ -40,8 +48,10 @@
},
"externalReferences": {
"description": "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI.",
"relationshipType": "one-to-many",
"items": {
"$ref": "../BrAPI-Common/ExternalReference.json#/$defs/ExternalReference"
"$ref": "../BrAPI-Common/ExternalReference.json#/$defs/ExternalReference",
"description": "ExternalReferences"
},
"title": "ExternalReferences",
"type": [
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14 changes: 12 additions & 2 deletions Specification/BrAPI-Schema/BrAPI-Core/List.json
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Expand Up @@ -4,7 +4,15 @@
"properties": {
"additionalInfo": {
"description": "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification.",
"$ref": "../BrAPI-Common/AdditionalInfo.json#/$defs/AdditionalInfo"
"relationshipType": "one-to-many",
"items": {
"$ref": "../BrAPI-Common/AdditionalInfo.json#/$defs/AdditionalInfo",
"description": "AdditionalInfo"
},
"type": [
"null",
"array"
]
},
"data": {
"description": "The array of DbIds of the BrAPI objects contained in a List",
Expand Down Expand Up @@ -35,8 +43,10 @@
},
"externalReferences": {
"description": "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI.",
"relationshipType": "one-to-many",
"items": {
"$ref": "../BrAPI-Common/ExternalReference.json#/$defs/ExternalReference"
"$ref": "../BrAPI-Common/ExternalReference.json#/$defs/ExternalReference",
"description": "ExternalReferences"
},
"title": "ExternalReferences",
"type": [
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14 changes: 12 additions & 2 deletions Specification/BrAPI-Schema/BrAPI-Core/Location.json
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Expand Up @@ -11,7 +11,15 @@
},
"additionalInfo": {
"description": "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification.",
"$ref": "../BrAPI-Common/AdditionalInfo.json#/$defs/AdditionalInfo"
"relationshipType": "one-to-many",
"items": {
"$ref": "../BrAPI-Common/AdditionalInfo.json#/$defs/AdditionalInfo",
"description": "AdditionalInfo"
},
"type": [
"null",
"array"
]
},
"coordinateDescription": {
"description": "Describes the precision and landmarks of the coordinate values used for a Location. (ex. the site, the nearest town, a 10 kilometers radius circle, +/- 20 meters, etc)",
Expand Down Expand Up @@ -69,8 +77,10 @@
},
"externalReferences": {
"description": "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI.",
"relationshipType": "one-to-many",
"items": {
"$ref": "../BrAPI-Common/ExternalReference.json#/$defs/ExternalReference"
"$ref": "../BrAPI-Common/ExternalReference.json#/$defs/ExternalReference",
"description": "ExternalReferences"
},
"title": "ExternalReferences",
"type": [
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14 changes: 12 additions & 2 deletions Specification/BrAPI-Schema/BrAPI-Core/Person.json
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Expand Up @@ -4,7 +4,15 @@
"properties": {
"additionalInfo": {
"description": "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification.",
"$ref": "../BrAPI-Common/AdditionalInfo.json#/$defs/AdditionalInfo"
"relationshipType": "one-to-many",
"items": {
"$ref": "../BrAPI-Common/AdditionalInfo.json#/$defs/AdditionalInfo",
"description": "AdditionalInfo"
},
"type": [
"null",
"array"
]
},
"description": {
"description": "description of this person",
Expand All @@ -22,8 +30,10 @@
},
"externalReferences": {
"description": "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI.",
"relationshipType": "one-to-many",
"items": {
"$ref": "../BrAPI-Common/ExternalReference.json#/$defs/ExternalReference"
"$ref": "../BrAPI-Common/ExternalReference.json#/$defs/ExternalReference",
"description": "ExternalReferences"
},
"title": "ExternalReferences",
"type": [
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14 changes: 12 additions & 2 deletions Specification/BrAPI-Schema/BrAPI-Core/Program.json
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Expand Up @@ -11,7 +11,15 @@
},
"additionalInfo": {
"description": "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification.",
"$ref": "../BrAPI-Common/AdditionalInfo.json#/$defs/AdditionalInfo"
"relationshipType": "one-to-many",
"items": {
"$ref": "../BrAPI-Common/AdditionalInfo.json#/$defs/AdditionalInfo",
"description": "AdditionalInfo"
},
"type": [
"null",
"array"
]
},
"commonCropName": {
"description": "Common name for the crop which this program is for",
Expand All @@ -30,8 +38,10 @@
},
"externalReferences": {
"description": "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI.",
"relationshipType": "one-to-many",
"items": {
"$ref": "../BrAPI-Common/ExternalReference.json#/$defs/ExternalReference"
"$ref": "../BrAPI-Common/ExternalReference.json#/$defs/ExternalReference",
"description": "ExternalReferences"
},
"title": "ExternalReferences",
"type": [
Expand Down
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