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Model separation #14

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Model separation #14

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53daea9
First separation of phenotype models
LzLang Apr 16, 2024
f51c665
First try for separation of models
LzLang Apr 16, 2024
ee656fb
BrAPI-Core model separation
VivianBass Apr 17, 2024
497eeb4
core and genotyping separate models. Location and allelematrix missing
VivianBass Apr 17, 2024
0fa4278
fixing ids and name models
VivianBass Apr 17, 2024
2b33307
First version of the separated models of germplasm
LzLang Apr 17, 2024
c1888e9
complete data separation of BrAPI-Core
VivianBass Apr 18, 2024
090f5a2
fix Sebastian observations
VivianBass Apr 18, 2024
1eaba4b
alleleMatrix data separation
VivianBass Apr 18, 2024
1ccb82b
Seperated models for Germplasm and Phenotyping Schema
LzLang Apr 18, 2024
9b0e25c
Merge pull request #13 from VivianBass/model_separation
LzLang Apr 18, 2024
c6f8d0d
optimizing data models
VivianBass Apr 18, 2024
7cbc97e
Add files via upload
LzLang Apr 18, 2024
36e622a
separate meta models
VivianBass Apr 18, 2024
25d45da
Merge branch 'model_separation' into model_separation
LzLang Apr 19, 2024
c6ddb81
Merge pull request #15 from VivianBass/model_separation
LzLang Apr 19, 2024
1201aa2
Unifying files
LzLang Apr 19, 2024
348f689
fix coordinates model
VivianBass May 27, 2024
beda6fb
Merge branch 'model_separation' into model_separation
VivianBass May 27, 2024
23f5c43
Merge pull request #17 from VivianBass/model_separation
LzLang May 28, 2024
c569b49
Delete BrAPI-Schema/BrAPI-Meta/Category.json
LzLang May 28, 2024
847b39a
Delete BrAPI-Schema/BrAPI-Meta/ValidValue.json
LzLang May 28, 2024
140b537
Unified primary keys in all models
LzLang May 28, 2024
08d9f80
Updated Version
LzLang Jun 18, 2024
746d477
Corrected some Typos
LzLang Jun 18, 2024
4559296
Corrected missing associations and tipos
LzLang Jul 24, 2024
8f639d7
Delete BrAPI-Schema/BrAPI-Meta/OntologyReference.json
LzLang Jul 26, 2024
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37 changes: 14 additions & 23 deletions BrAPI-Schema/BrAPI-Core/List.json
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Original file line number Diff line number Diff line change
Expand Up @@ -3,13 +3,17 @@
"List": {
"properties": {
"additionalInfo": {
"additionalProperties": {
"type": "string"
},
"title": "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.",
"referencedAttribute": "list",
"relationshipType": "one-to-many",
"items": {
"$ref": "AdditionalInfo.json#/$defs/AdditionalInfo",
"description": "AdditionalInfo"
},
"type": [
"null",
"object"
"array"
]
},
"data": {
Expand Down Expand Up @@ -40,27 +44,14 @@
]
},
"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.",
"title": "externalReferences",
"description": "The ID which uniquely identifies this external reference field",
"referencedAttribute": "list",
"relationshipType": "one-to-many",
"items": {
"properties": {
"referenceId": {
"description": "The external reference ID. Could be a simple string or a URI.",
"type": [
"null",
"string"
]
},
"referenceSource": {
"description": "An identifier for the source system or database of this reference",
"type": [
"null",
"string"
]
}
},
"type": "object"
"$ref": "ExternalReference.json#/$defs/ExternalReference",
"description": "externalReferences"
},
"title": "ExternalReferences",
"type": [
"null",
"array"
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133 changes: 25 additions & 108 deletions BrAPI-Schema/BrAPI-Core/Location.json
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Expand Up @@ -10,13 +10,17 @@
]
},
"additionalInfo": {
"additionalProperties": {
"type": "string"
},
"title": "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.",
"referencedAttribute": "location",
"relationshipType": "one-to-many",
"items": {
"$ref": "AdditionalInfo.json#/$defs/AdditionalInfo",
"description": "AdditionalInfo"
},
"type": [
"null",
"object"
"array"
]
},
"coordinateDescription": {
Expand All @@ -34,88 +38,12 @@
]
},
"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.",
"properties": {
"geometry": {
"description": "A geometry as defined by GeoJSON (RFC 7946). In this context, only Point or Polygon geometry are allowed.",
"oneOf": [
{
"description": "Copied 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": {
"coordinates": {
"description": "A single position",
"items": {
"type": "number"
},
"minItems": 2,
"type": "array"
},
"type": {
"default": "Point",
"description": "The literal string \"Point\"",
"type": "string"
}
},
"required": [
"type",
"coordinates"
],
"type": "object"
},
{
"description": "An array of Linear Rings. Each Linear Ring is an array of Points. \n\nA Point 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": {
"coordinates": {
"description": "An array of linear rings",
"items": {
"description": "An array of at least four positions where the first equals the last",
"items": {
"description": "A single position",
"items": {
"type": "number"
},
"minItems": 2,
"type": "array"
},
"minItems": 4,
"type": "array"
},
"type": "array"
},
"type": {
"default": "Polygon",
"description": "The literal string \"Polygon\"",
"type": "string"
}
},
"required": [
"type",
"coordinates"
],
"type": "object"
}
],
"title": "GeoJSON Geometry",
"type": [
"null",
"object"
]
},
"type": {
"default": "Feature",
"description": "The literal string \"Feature\"",
"type": [
"null",
"string"
]
}
},
"title": "GeoJSON",
"type": [
"null",
"object"
]
"$ref": "Coordinate.json#/$defs/Coordinate",
"description": "The ID which uniquely identifies this coordinate field",
"referencedAttribute": "location",
"relationshipType": "one-to-one"
},

"countryCode": {
"description": "[ISO_3166-1_alpha-3](https://en.wikipedia.org/wiki/ISO_3166-1_alpha-3) spec\n<br/> MIAPPE V1.1 (DM-17) Geographic location (country) - The country where the experiment took place, either as a full name or preferably as a 2-letter code.'",
"type": [
Expand Down Expand Up @@ -153,32 +81,20 @@
]
},
"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.",
"title": "externalReferences",
"description": "The ID which uniquely identifies this external reference field",
"referencedAttribute": "location",
"relationshipType": "one-to-many",
"items": {
"properties": {
"referenceId": {
"description": "The external reference ID. Could be a simple string or a URI.",
"type": [
"null",
"string"
]
},
"referenceSource": {
"description": "An identifier for the source system or database of this reference",
"type": [
"null",
"string"
]
}
},
"type": "object"
"$ref": "ExternalReference.json#/$defs/ExternalReference",
"description": "externalReferences"
},
"title": "ExternalReferences",
"type": [
"null",
"array"
]
},

"instituteAddress": {
"description": "The street address of the institute at a particular Location\n<br/> MIAPPE V1.1 (DM-16) Contact institution - Name and address of the institution responsible for the study.",
"type": [
Expand Down Expand Up @@ -216,7 +132,7 @@
},
"childLocations": {
"title": "ChildLocations",
"description": "",
"description": "The ID which uniquely identifies this child location field",
"referencedAttribute": "parentLocation",
"relationshipType": "one-to-many",
"items": {
Expand All @@ -230,7 +146,7 @@
},
"studies": {
"title": "Studies",
"description": "",
"description": "The ID which uniquely identifies this study field",
"referencedAttribute": "location",
"relationshipType": "one-to-many",
"items": {
Expand Down Expand Up @@ -265,7 +181,7 @@
},
"seedLots": {
"title": "seedLots",
"description": "seedLots",
"description": "The ID which uniquely identifies this seed lot field",
"referencedAttribute": "location",
"relationshipType": "one-to-many",
"items": {
Expand All @@ -279,7 +195,7 @@
},
"observationUnits": {
"title": "observationUnits",
"description": "observationUnits",
"description": "The ID which uniquely identifies this observation Unit field",
"referencedAttribute": "location",
"relationshipType": "one-to-many",
"items": {
Expand All @@ -299,6 +215,7 @@
"title": "Location",
"type": "object"
}

},
"$id": "https://brapi.org/Specification/BrAPI-Schema/BrAPI-Core/Location.json",
"$schema": "http://json-schema.org/draft/2020-12/schema"
Expand Down
41 changes: 16 additions & 25 deletions BrAPI-Schema/BrAPI-Core/Person.json
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Original file line number Diff line number Diff line change
Expand Up @@ -3,13 +3,17 @@
"Person": {
"properties": {
"additionalInfo": {
"additionalProperties": {
"type": "string"
},
"title": "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.",
"referencedAttribute": "person",
"relationshipType": "one-to-many",
"items": {
"$ref": "AdditionalInfo.json#/$defs/AdditionalInfo",
"description": "AdditionalInfo"
},
"type": [
"null",
"object"
"array"
]
},
"description": {
Expand All @@ -27,27 +31,14 @@
]
},
"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.",
"title": "externalReferences",
"description": "The ID which uniquely identifies this external reference field",
"referencedAttribute": "person",
"relationshipType": "one-to-many",
"items": {
"properties": {
"referenceId": {
"description": "The external reference ID. Could be a simple string or a URI.",
"type": [
"null",
"string"
]
},
"referenceSource": {
"description": "An identifier for the source system or database of this reference",
"type": [
"null",
"string"
]
}
},
"type": "object"
"$ref": "ExternalReference.json#/$defs/ExternalReference",
"description": "externalReferences"
},
"title": "ExternalReferences",
"type": [
"null",
"array"
Expand Down Expand Up @@ -101,7 +92,7 @@
},
"lists": {
"title": "Lists",
"description": "",
"description": "The ID which uniquely identifies this list field",
"referencedAttribute": "listOwnerPerson",
"relationshipType": "one-to-many",
"items": {
Expand All @@ -115,7 +106,7 @@
},
"programs": {
"title": "Programs",
"description": "",
"description": "The ID which uniquely identifies this program field",
"referencedAttribute": "leadPerson",
"relationshipType": "one-to-many",
"items": {
Expand Down
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