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Guy Davenport
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Merge branch 'brapi-V2.2' into 649-merge-generator-changes-into-v2_2-fix-the-misplacement-of-a-nullable-tag-and-remove-the-out-directory
# Conflicts: # Specification/BrAPI-Core/Studies/README.md # Specification/Generated/BrAPI-Core.yaml # Specification/Generated/BrAPI-Genotyping.yaml # Specification/Generated/BrAPI-Germplasm.yaml # Specification/Generated/BrAPI-Phenotyping.yaml # Specification/Generated/brapi_generated.graphqls # Specification/Generated/brapi_generated.json # Specification/Generated/brapi_generated.ttl # Specification/Generated/brapi_openapi.json # Specification/Generated/brapi_openapi_comparison.md
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‎Specification/BrAPI-Core/Studies/README.md‎

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‎Specification/BrAPI-Core/Studies/Schemas/StudyNewRequest.yaml‎

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nullable: true
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example: Irrigation was applied according needs during summer to prevent water stress.
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experimentalDesign:
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description: The experimental and statistical design full description plus a category PUI taken from crop research ontology or agronomy ontology
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type: object
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$ref: '#/components/schemas/ExperimentalDesign'
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nullable: true
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properties:
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description:
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description: MIAPPE V1.1 (DM-22) Description of the experimental design - Short description of the experimental design, possibly including statistical design. In specific cases, e.g. legacy datasets or data computed from several studies, the experimental design can be "unknown"/"NA", "aggregated/reduced data", or simply 'none'.
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type: string
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nullable: true
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example: Lines were repeated twice at each location using a complete block design. In order to limit competition effects, each block was organized into four sub-blocks corresponding to earliest groups based on a prior information.
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PUI:
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description: MIAPPE V1.1 (DM-23) Type of experimental design - Type of experimental design of the study, in the form of an accession number from the Crop Ontology.
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type: string
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nullable: true
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example: CO_715:0000145
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growthFacility:
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description: Short description of the facility in which the study was carried out.
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type: object

‎Specification/BrAPI-Phenotyping/ObservationUnits/README.md‎

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‎Specification/BrAPI-Phenotyping/ObservationUnits/Schemas/ObservationTreatment.yaml‎

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@@ -11,17 +11,28 @@ components:
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factor:
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description: |-
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The type of treatment/factor. ex. 'fertilizer', 'inoculation', 'irrigation', etc
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MIAPPE V1.1 (DM-61) Experimental Factor type - Name/Acronym of the experimental factor.
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type: string
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nullable: true
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deprecated: true
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example: fertilizer
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factorPUI:
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description: |-
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The PUI of the factor which may link to an ontology
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type: string
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nullable: true
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example: test-factor:dia2020-2-nv.fertilizer
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modality:
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description: |-
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The treatment/factor description. ex. 'low fertilizer', 'yellow rust inoculation', 'high water', etc
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MIAPPE V1.1 (DM-62) Experimental Factor description - Free text description of the experimental factor. This includes all relevant treatments planned and protocol planned for all the plants targeted by a given experimental factor.
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MIAPPE V1.1 (DM-62) Experimental Factor description - Free text description of the experimental factor. This includes all relevant treatments planned and protocol planned for all the plants targeted by a given experimental factor.
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type: string
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nullable: true
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deprecated: true
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example: low fertilizer
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modalityPUI:
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description: |-
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The PUI of the modality which may link to an ontology
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type: string
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nullable: true
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example: test-factor:dia2020-2-nv.lf

‎Specification/BrAPI-Schema/BrAPI-Core/Study.json‎

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"ExperimentalDesign": {
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"properties": {
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"PUI": {
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"description": "MIAPPE V1.1 (DM-23) Type of experimental design - Type of experimental design of the study, in the form of an accession number from the Crop Ontology. **Deprecated in v2.2** Please use `experimentalDesignPUI`. Github issue number #539",
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"type": [
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"null",
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"string"
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],
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"deprecated": true
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},
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"experimentalDesignPUI": {
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"description": "MIAPPE V1.1 (DM-23) Type of experimental design - Type of experimental design of the study, in the form of an accession number from the Crop Ontology.",
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"type": [
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"null",
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"string"
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]
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],
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"examples": ["CO_715:0000145"]
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},
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"description": {
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"description": "MIAPPE V1.1 (DM-22) Description of the experimental design - Short description of the experimental design, possibly including statistical design. In specific cases, e.g. legacy datasets or data computed from several studies, the experimental design can be \"unknown\"/\"NA\", \"aggregated/reduced data\", or simply 'none'.",
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"string"
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]
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},
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"randomizationType": {
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"description": "The type of randomization use to create the experimental design.",
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"type": [
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"null",
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"string"
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],
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"examples": ["RCB:Randomize Complete Block"]
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},
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"layoutPattern": {
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"description": "How the trial is layout in the field.",
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"type": [
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"null",
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"string"
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],
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"examples": ["Serpentine"]
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},
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"setSize": {
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"description": "The size of the sets in the design.",
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"type": [
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"null",
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"number"
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],
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"examples": [1]
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},
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"rowsPerPlot": {
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"description": "The number of rows in a plot.",
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"type": [
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"null",
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"number"
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],
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"examples": [1]
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},
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"firstRepRand": {
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"description": "Is the first replication random.",
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"type": [
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"null",
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"boolean"
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],
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"examples": [true]
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},
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"experimentFactors": {
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"description": "The factors used in the experimental design.",
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"items": {
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"$ref": "../BrAPI-Core/Study.json#/$defs/ExperimentFactor"
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},
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"type": [
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"null",
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"array"
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]
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},
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"study": {
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"description": "Experimental design associated with a study",
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"$ref": "../BrAPI-Core/Study.json#/$defs/Study",
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"primaryModel": false
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}
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},
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"ExperimentFactor": {
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"properties": {
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"factor": {
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"description": "The type of treatment/factor. ex. 'fertilizer', 'inoculation', 'irrigation', etc\n\nMIAPPE V1.1 (DM-61) Experimental Factor type - Name/Acronym of the experimental factor.",
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"type": "string",
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"examples": [
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"fertilizer"
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]
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},
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"factorPUI": {
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"description": "The PUI of the factor which may link to an ontology.",
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"type": [
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"null",
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"string"
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],
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"examples": [
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"test-factor:dia2020-2-nv.fertilizer"
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]
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},
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"modalities": {
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"description": "The type of treatment/factor. ex. 'fertilizer', 'inoculation', 'irrigation', etc\n\nMIAPPE V1.1 (DM-61) Experimental Factor type - Name/Acronym of the experimental factor.",
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"items": {
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"type": "object",
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"properties": {
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"modality": {
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"description": "The treatment/factor description. ex. 'low fertilizer', 'yellow rust inoculation', 'high water', etc\n\nMIAPPE V1.1 (DM-62) Experimental Factor description - Free text description of the experimental factor. This includes all relevant treatments planned and protocol planned for all the plants targeted by a given experimental factor. ",
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"type": "string",
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"examples": [
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"low fertilizer"
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]
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},
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"modalityPUI": {
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"description": "The PUI of the modality which may link to an ontology.",
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"type": [
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"null",
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"string"
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],
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"examples": [
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"test-factor:dia2020-2-nv.lf"
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]
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}
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}
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},
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"type": [
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"null",
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"array"
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],
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"examples": [
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"fertilizer"
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]
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}
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},
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"title": "ExperimentFactor",
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"type": "object",
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"brapi-metadata": {
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"primaryModel": false
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}
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},
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"GrowthFacility": {
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"properties": {
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"PUI": {

‎Specification/BrAPI-Schema/BrAPI-Phenotyping/ObservationUnit.json‎

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"observationUnitDbId"
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],
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"title": "ObservationUnit",
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"description": "A representation of the physical entity being observed during a phenotype data collection process. Typically, this is a Plot or a Plant, but it could include things like Fields, Blocks, or Samples.",
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"type": "object",
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"brapi-metadata": {
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"primaryModel": true
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"primaryModel": false
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}
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},
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"Treatment": {
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"ObservationTreatment": {
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"properties": {
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"factor": {
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"description": "The type of treatment/factor. ex. 'fertilizer', 'inoculation', 'irrigation', etc\n\nMIAPPE V1.1 (DM-61) Experimental Factor type - Name/Acronym of the experimental factor.",
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"type": [
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"null",
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"string"
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]
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],
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"examples": ["test-factor:dia2020-2-nv.fertilizer"]
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},
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"modality": {
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"description": "The treatment/factor description. ex. 'low fertilizer', 'yellow rust inoculation', 'high water', etc\n\nMIAPPE V1.1 (DM-62) Experimental Factor description - Free text description of the experimental factor. This includes all relevant treatments planned and protocol planned for all the plants targeted by a given experimental factor. ",
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"type": [
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"null",
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"string"
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]
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],
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"examples": ["test-factor:dia2020-2-nv.lf"]
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},
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"observationUnit": {
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"description": "associated observation Unit",
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"referencedAttribute": "treatments"
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}
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},
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"title": "Treatment",
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"title": "ObservationTreatment",
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"description": "The type of treatment/factor. ex. 'fertilizer', 'inoculation', 'irrigation', etc. MIAPPE V1.1 (DM-61) Experimental Factor type - Name/Acronym of the experimental factor.",
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"type": "object",
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"brapi-metadata": {

‎Specification/Components/Schemas/ExperimentalDesign.yaml‎

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info:
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title: BrAPI
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version: ''
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openapi: 3.0.0
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paths: {}
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components:
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schemas:
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ExperimentalDesign:
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title: ExperimentalDesign
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type: object
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description: |-
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The experimental and statistical design full description plus a category PUI taken from crop research ontology or agronomy ontology
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properties:
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description:
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description: MIAPPE V1.1 (DM-22) Description of the experimental design - Short description of the experimental design, possibly including statistical design. In specific cases, e.g. legacy datasets or data computed from several studies, the experimental design can be "unknown"/"NA", "aggregated/reduced data", or simply 'none'.
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type: string
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nullable: true
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example: Lines were repeated twice at each location using a complete block design. In order to limit competition effects, each block was organized into four sub-blocks corresponding to earliest groups based on a prior information.
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PUI:
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description: |-
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MIAPPE V1.1 (DM-23) Type of experimental design - Type of experimental design of the study, in the form of an accession number from the Crop Ontology.
22+
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**Deprecated in v2.2** Please use `experimentalDesignPUI`. Github issue number #539
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type: string
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deprecated: true
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nullable: true
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example: CO_715:0000145
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experimentalDesignPUI:
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description: MIAPPE V1.1 (DM-23) Type of experimental design - Type of experimental design of the study, in the form of an accession number from the Crop Ontology.
30+
type: string
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nullable: true
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example: CO_715:0000145
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randomizationType:
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description: The type of randomization use to create the experimental design
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type: string
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nullable: true
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example: RCB:Randomize Complete Block
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layoutPattern:
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description: How the trial is layout in the field
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type: string
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nullable: true
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example: Serpentine
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setSize:
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description: The size of the sets in the design
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type: number
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nullable: true
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example: 1
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rowsPerPlot:
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description: The number of rows in a plot
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type: number
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nullable: true
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example: 1
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firstRepRand:
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description: Is the first replication random
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type: boolean
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nullable: true
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example: true
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experimentFactors:
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description: |-
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The factors used in the experimental design
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type: array
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nullable: true
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items:
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type: object
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title: "ExperimentFactor"
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properties:
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factor:
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description: |-
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The type of treatment/factor. For example 'fertilizer', 'inoculation', 'irrigation', etc
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MIAPPE V1.1 (DM-61) Experimental Factor type - Name/Acronym of the experimental factor.
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type: string
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example: fertilizer
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factorPUI:
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description: |-
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The PUI of the factor which may link to an ontology
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type: string
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nullable: true
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example: test-factor:dia2020-2-nv.fertilizer
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modalities:
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items:
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type: object
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properties:
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modality:
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description: |-
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The treatment/factor modality or level. For example 'low fertilizer', 'yellow rust inoculation', 'high water', etc
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MIAPPE V1.1 (DM-62) Experimental Factor description - Free text description of the experimental factor. This includes all relevant treatments planned and protocol planned for all the plants targeted by a given experimental factor.
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type: string
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example: low fertilizer
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modalityPUI:
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description: |-
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The PUI of the modality which may link to an ontology
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type: string
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nullable: true
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example: test-factor:dia2020-2-nv.lf

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