Merge pull request #613 from plantbreeding/LzLang-patch-1

One-dimensionalization of data models
plantbreeding · Oct 15, 2024 · e60eaaf · e60eaaf
2 parents ad8d942 + 22a9de9
commit e60eaaf
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diff --git a/Specification/BrAPI-Schema/BrAPI-Common/ExternalReference.json b/Specification/BrAPI-Schema/BrAPI-Common/ExternalReference.json
@@ -2,7 +2,7 @@
     "$defs": {
         "ExternalReference": {
             "properties": {
-                "referenceId": {
+                "externalReferenceDbId": {
                     "description": "The external reference ID. Could be a simple string or a URI.",
                     "type": [
                         "null",

diff --git a/Specification/BrAPI-Schema/BrAPI-Common/GeoJSON.json b/Specification/BrAPI-Schema/BrAPI-Common/GeoJSON.json
@@ -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": {
+                "geoJSONDbId": {
+                    "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"
@@ -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": [
+                "geoJSONDbId"
+            ]
         }
     },
     "$id": "https://brapi.org/Specification/BrAPI-Schema/BrAPI-Common/GeoJSON.json",

diff --git a/Specification/BrAPI-Schema/BrAPI-Common/SourceGermplasm.json b/Specification/BrAPI-Schema/BrAPI-Common/SourceGermplasm.json
@@ -0,0 +1,34 @@
+{
+    "$defs": {
+        "SourceGermplasm": {
+            "properties": {
+                "germplasmName": {
+                    "description": "The human readable name of a `Germplasm`",
+                    "type": [
+                        "null",
+                        "string"
+                    ]
+                },
+                "reference": {
+                    "description": "Germplasm associated with a reference",
+                    "$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#/$defs/ReferenceSet",
+                    "relationshipType": "many-to-one",
+                    "referencedAttribute": "sourceGermplasm"
+                }
+            },
+            "title": "sourceGermplasm",
+            "type": "object",
+            "brapi-metadata": {
+                "primaryModel": false
+            }
+        }
+    },
+    "$id": "https://brapi.org/Specification/BrAPI-Schema/BrAPI-Common/SourceGermplasm.json",
+    "$schema": "http://json-schema.org/draft/2020-12/schema"
+}
diff --git a/Specification/BrAPI-Schema/BrAPI-Common/Species.json b/Specification/BrAPI-Schema/BrAPI-Common/Species.json
@@ -0,0 +1,51 @@
+{
+    "$defs": {
+        "Species": {
+            "properties": {
+                "speciesDbId": {
+                    "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"
+}
diff --git a/Specification/BrAPI-Schema/BrAPI-Common/TraitDataType.json b/Specification/BrAPI-Schema/BrAPI-Common/TraitDataType.json
@@ -15,6 +15,6 @@
             "example": "Numerical"
         }
     },
-    "$id": "https://brapi.org/Specification/BrAPI-Schema/Components/Common/AdditionalInfo.json",
+    "$id": "https://brapi.org/Specification/BrAPI-Schema/Components/Common/TraitDataType.json",
     "$schema": "http://json-schema.org/draft/2020-12/schema"
 }
diff --git a/Specification/BrAPI-Schema/BrAPI-Common/Variable.json b/Specification/BrAPI-Schema/BrAPI-Common/Variable.json
@@ -2,9 +2,17 @@
     "$defs": {
         "Variable": {
             "properties": {
+				"variableDbId": {
+                    "description": "Unique identifier for the Variable",
+                    "type": [
+                        "null",
+                        "string"
+                    ]
+                },
                 "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"
+                    "$ref": "../BrAPI-Common/AdditionalInfo.json#/$defs/AdditionalInfo",
+					"relationshipType": "one-to-one"
                 },
                 "commonCropName": {
                     "description": "Crop name (examples: \"Maize\", \"Wheat\")",
@@ -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": [
@@ -72,14 +82,17 @@
                 },
                 "method": {
                     "description": "A description of the way an Observation should be collected. \n<br>For example, an ObservationVariable might be defined with a Trait of \"plant height\", a Scale of \"meters\", and a Method of \"tape measure\". This variable would be distinct from a variable with the Method \"estimation\" or \"drone image processing\". ",
+					"relationshipType": "one-to-one",
                     "$ref": "../BrAPI-Phenotyping/Method.json#/$defs/Method"
                 },
                 "ontologyReference": {
                     "description": "MIAPPE V1.1\n\n(DM-85) Variable accession number - Accession number of the variable in the Crop Ontology\n\n(DM-87) Trait accession number - Accession number of the trait in a suitable controlled vocabulary (Crop Ontology, Trait Ontology).\n\n(DM-89) Method accession number - Accession number of the method in a suitable controlled vocabulary (Crop Ontology, Trait Ontology).\n\n(DM-93) Scale accession number - Accession number of the scale in a suitable controlled vocabulary (Crop Ontology).",
+                    "relationshipType": "one-to-one",
                     "$ref": "../BrAPI-Phenotyping/OntologyReference.json#/$defs/OntologyReference"
                 },
                 "scale": {
                     "description": "A Scale describes the units and acceptable values for an ObservationVariable. \n<br>For example, an ObservationVariable might be defined with a Trait of \"plant height\", a Scale of \"meters\", and a Method of \"tape measure\". This variable would be distinct from a variable with the Scale \"inches\" or \"pixels\".",
+                    "relationshipType": "one-to-one",
                     "$ref": "../BrAPI-Phenotyping/Scale.json#/$defs/Scale"
                 },
                 "scientist": {
@@ -116,6 +129,7 @@
                 },
                 "trait": {
                     "description": "A Trait describes what property is being observed. \n<br>For example, an ObservationVariable might be defined with a Trait of \"plant height\", a Scale of \"meters\", and a Method of \"tape measure\". This variable would be distinct from a variable with the Trait \"Leaf length\" or \"Flower height\". ",
+                    "relationshipType": "one-to-one",
                     "$ref": "../BrAPI-Phenotyping/Trait.json#/$defs/Trait"
                 }
             },

diff --git a/Specification/BrAPI-Schema/BrAPI-Core/List.json b/Specification/BrAPI-Schema/BrAPI-Core/List.json
@@ -4,7 +4,8 @@
             "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"
+                    "$ref": "../BrAPI-Common/AdditionalInfo.json#/$defs/AdditionalInfo",
+					"relationshipType": "one-to-one"
                 },
                 "data": {
                     "description": "The array of DbIds of the BrAPI objects contained in a List",
@@ -35,8 +36,10 @@
                 },
                 "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": [

diff --git a/Specification/BrAPI-Schema/BrAPI-Core/Location.json b/Specification/BrAPI-Schema/BrAPI-Core/Location.json
@@ -11,7 +11,8 @@
                 },
                 "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"
+                    "$ref": "../BrAPI-Common/AdditionalInfo.json#/$defs/AdditionalInfo",
+					"relationshipType": "one-to-one"
                 },
                 "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)",
@@ -29,6 +30,7 @@
                 },
                 "coordinates": {
                     "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.",
+                    "relationshipType": "one-to-one",
                     "$ref": "../BrAPI-Common/GeoJSON.json#/$defs/GeoJSON"
                 },
                 "countryCode": {
@@ -69,8 +71,10 @@
                 },
                 "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": [

diff --git a/Specification/BrAPI-Schema/BrAPI-Core/Person.json b/Specification/BrAPI-Schema/BrAPI-Core/Person.json
@@ -4,7 +4,8 @@
             "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"
+                    "$ref": "../BrAPI-Common/AdditionalInfo.json#/$defs/AdditionalInfo",
+					"relationshipType": "one-to-one"
                 },
                 "description": {
                     "description": "description of this person",
@@ -22,8 +23,10 @@
                 },
                 "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": [

diff --git a/Specification/BrAPI-Schema/BrAPI-Core/Program.json b/Specification/BrAPI-Schema/BrAPI-Core/Program.json
@@ -11,7 +11,8 @@
                 },
                 "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"
+                    "$ref": "../BrAPI-Common/AdditionalInfo.json#/$defs/AdditionalInfo",
+					"relationshipType": "one-to-one"
                 },
                 "commonCropName": {
                     "description": "Common name for the crop which this program is for",
@@ -30,8 +31,10 @@
                 },
                 "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": [