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Guy Davenport
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‎Scripts/buildDocs.sh‎

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@@ -58,7 +58,7 @@ python3 ./Scripts/buildBlueprint.py -out "./Specification/BrAPI-Genotyping/" -he
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echo
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echo "Build complete OpenAPI in one YAML file: ./brapi_openapi.yaml for sharing."
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python3 ./Scripts/buildOpenAPI.py ./Specification/swaggerBrAPIPlusMetaData.yaml ./Specification/BrAPI-Core/ ./Specification/BrAPI-Germplasm/ ./Specification/BrAPI-Genotyping/ ./Specification/BrAPI-Phenotyping/ ./Specification/Components >> ./build/results/buildOpenAPICompleteResults.txt
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python3 ./Scripts/buildOpenAPI.py ./Specification/swaggerMetaData.yaml ./Specification/BrAPI-Core/ ./Specification/BrAPI-Germplasm/ ./Specification/BrAPI-Genotyping/ ./Specification/BrAPI-Phenotyping/ ./Specification/Components >> ./build/results/buildOpenAPICompleteResults.txt
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cp ./Specification/BrAPI-Core/brapi_openapi.yaml ./build/brapi_openapi.yaml
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‎Specification/swaggerMetaData.yaml‎

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components:
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securitySchemes:
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AuthorizationToken:
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bearerFormat: nonce token or JWT
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description: OAuth Bearer Token - A valid Bearer token to prove authorization
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scheme: bearer
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type: http
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info:
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description: |-
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The Breeding API (BrAPI) is a Standardized REST ful Web Service API Specification for communicating Plant Breeding Data. BrAPI allows for easy data sharing between databases and tools involved in plant breeding.
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<div class="brapi-section">
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<h2 class="brapi-section-title">General Reference Documentation</h2>
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<div class="gen-info-link"><a href="https://wiki.brapi.org/index.php/RESTfulness">URL Structure</a></div>
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<div class="gen-info-link"><a href="https://wiki.brapi.org/index.php/Response_Structure">Response Structure</a></div>
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<div class="gen-info-link"><a href="https://wiki.brapi.org/index.php/Dates_and_Times">Date/Time Encoding</a></div>
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<div class="gen-info-link"><a href="https://wiki.brapi.org/index.php/Location_Coordinates">Location Encoding</a></div>
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<div class="gen-info-link"><a href="https://wiki.brapi.org/index.php/Error_Handling">Error Handling</a></div>
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<div class="gen-info-link"><a href="https://wiki.brapi.org/index.php/Search_Services">Search Services</a></div>
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</div>
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<div class="current-brapi-section brapi-section">
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<h2 class="brapi-section-title">BrAPI Core</h2>
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<div class="brapi-section-description">The BrAPI Core module contains high level entities used for organization and management. This includes Programs, Trials, Studies, Locations, People, and Lists</div>
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<div class="version-number">V2.1</div>
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<div class="link-btn"><a href="https://github.com/plantbreeding/API/tree/brapi-V2.1/Specification/BrAPI-Core">GitHub</a></div>
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<div class="link-btn"><a href="https://app.swaggerhub.com/apis/PlantBreedingAPI/BrAPI-Core/2.1">SwaggerHub</a></div>
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<div class="link-btn"><a href="https://brapicore21.docs.apiary.io">Apiary</a></div>
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<div class="version-number">V2.0</div>
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<div class="link-btn"><a href="https://github.com/plantbreeding/API/tree/brapi-V2.0/Specification/BrAPI-Core">GitHub</a></div>
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<div class="link-btn"><a href="https://app.swaggerhub.com/apis/PlantBreedingAPI/BrAPI-Core/2.0">SwaggerHub</a></div>
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<div class="link-btn"><a href="https://brapicore20.docs.apiary.io">Apiary</a></div>
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<div class="stop-float"></div>
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</div>
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<div class="brapi-section">
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<h2 class="brapi-section-title">BrAPI Phenotyping</h2>
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<div class="brapi-section-description">The BrAPI Phenotyping module contains entities related to phenotypic observations. This includes Observation Units, Observations, Observation Variables, Traits, Scales, Methods, and Images</div>
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<div class="version-number">V2.1</div>
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<div class="link-btn"><a href="https://github.com/plantbreeding/API/tree/brapi-V2.1/Specification/BrAPI-Phenotyping">GitHub</a></div>
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<div class="link-btn"><a href="https://app.swaggerhub.com/apis/PlantBreedingAPI/BrAPI-Phenotyping/2.1">SwaggerHub</a></div>
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<div class="link-btn"><a href="https://brapiphenotyping21.docs.apiary.io">Apiary</a></div>
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<div class="stop-float"></div>
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</div>
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<div class="brapi-section">
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<h2 class="brapi-section-title">BrAPI Genotyping</h2>
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<div class="brapi-section-description">The BrAPI Genotyping module contains entities related to genotyping analysis. This includes Samples, Markers, Variant Sets, Variants, Call Sets, Calls, References, Reads, and Vendor Orders</div>
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<div class="version-number">V2.1</div>
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<div class="link-btn"><a href="https://github.com/plantbreeding/API/tree/brapi-V2.1/Specification/BrAPI-Genotyping">GitHub</a></div>
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<div class="link-btn"><a href="https://app.swaggerhub.com/apis/PlantBreedingAPI/BrAPI-Genotyping/2.1">SwaggerHub</a></div>
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<div class="link-btn"><a href="https://brapigenotyping21.docs.apiary.io">Apiary</a></div>
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<div class="stop-float"></div>
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</div>
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<div class="brapi-section">
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<h2 class="brapi-section-title">BrAPI Germplasm</h2>
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<div class="brapi-section-description">The BrAPI Germplasm module contains entities related to germplasm management. This includes Germplasm, Germplasm Attributes, Seed Lots, Crosses, Pedigree, and Progeny</div>
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<div class="version-number">V2.1</div>
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<div class="link-btn"><a href="https://github.com/plantbreeding/API/tree/brapi-V2.1/Specification/BrAPI-Germplasm">GitHub</a></div>
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<div class="link-btn"><a href="https://app.swaggerhub.com/apis/PlantBreedingAPI/BrAPI-Germplasm/2.1">SwaggerHub</a></div>
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<div class="link-btn"><a href="https://brapigermplasm21.docs.apiary.io">Apiary</a></div>
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<div class="stop-float"></div>
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</div>
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<style>
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.link-btn{
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float: left;
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margin: 2px 10px 0 0;
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padding: 0 5px;
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border-radius: 5px;
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background-color: #ddd;
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}
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.stop-float{
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clear: both;
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}
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.version-number{
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float: left;
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margin: 5px 10px 0 5px;
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}
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.brapi-section-title{
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margin: 0 10px 0 0;
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font-size: 20px;
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}
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.current-brapi-section{
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font-weight: bolder;
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border-radius: 5px;
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background-color: #ddd;
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}
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.brapi-section{
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padding: 5px 5px;
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}
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.brapi-section-description{
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margin: 5px 0 0 5px;
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}
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</style>
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title: BrAPI-Core
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version: '2.1'
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openapi: 3.0.0
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paths: {}
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security:
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- AuthorizationToken: []
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servers:
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- url: https://test-server.brapi.org/brapi/v2
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tags:
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- name: Server Info
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description: Check the available calls on a server
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externalDocs:
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description: Docs
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url: https://wiki.brapi.org/
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- name: Common Crop Names
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description: List of crops supported by this server
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externalDocs:
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description: Docs
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url: https://wiki.brapi.org/
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- name: Programs
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description: Information about Programs
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externalDocs:
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description: Docs
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url: https://wiki.brapi.org/
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- name: Trials
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description: Information about Trials
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externalDocs:
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description: Docs
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url: https://wiki.brapi.org/
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- name: Studies
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description: Information about Studies
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externalDocs:
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description: Docs
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url: https://wiki.brapi.org/
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- name: Locations
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description: Information about Locations
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externalDocs:
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description: Docs
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url: https://wiki.brapi.org/
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- name: Seasons
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description: Information about Seasons
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externalDocs:
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description: Docs
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url: https://wiki.brapi.org/
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- name: Lists
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description: Create and manipulate generic lists
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externalDocs:
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description: Docs
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url: https://wiki.brapi.org/
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- name: People
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description: Create and manipulate information about people
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externalDocs:
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description: Docs
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url: https://wiki.brapi.org/
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- name: Calls
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description: Individual genotype allele calls
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externalDocs:
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description: Docs
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url: https://wiki.brapi.org/
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- name: Call Sets
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description: Each Call Set is related to one physical sample
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externalDocs:
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description: Docs
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url: https://wiki.brapi.org/
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- name: Variants
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description: Information about Variants, also called Markers
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externalDocs:
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description: Docs
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url: https://wiki.brapi.org/
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- name: Variant Sets
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description: Information about Variant Sets, also called Data Sets or Allele Matrices
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externalDocs:
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description: Docs
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url: https://wiki.brapi.org/
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- name: Plates
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description: Information about plates containing samples
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externalDocs:
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description: Docs
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url: https://wiki.brapi.org/
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- name: Samples
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description: Information about physical samples
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externalDocs:
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description: Docs
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url: https://wiki.brapi.org/
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- name: References
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description: Genetic sequences used for reference
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externalDocs:
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description: Docs
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url: https://wiki.brapi.org/
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- name: Reference Sets
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description: Collections of references
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externalDocs:
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description: Docs
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url: https://wiki.brapi.org/
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- name: Genome Maps
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description: Information about physical and genetic maps
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externalDocs:
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description: Docs
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url: https://wiki.brapi.org/
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- name: Vendor
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description: This interface is specific to facilities that performs an external analysis, such as genotyping facilities. The interface should be implemented by that facility''s server. The breeding database is the client of this interface.
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externalDocs:
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description: Docs
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url: https://wiki.brapi.org/
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- name: Germplasm
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description: Information about Germplasm
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externalDocs:
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description: Docs
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url: https://wiki.brapi.org/
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- name: Germplasm Attributes
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description: Information about Germplasm Attributes
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externalDocs:
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description: Docs
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url: https://wiki.brapi.org/
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- name: Germplasm Attribute Values
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description: Information about Germplasm Attribute Values
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externalDocs:
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description: Docs
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url: https://wiki.brapi.org/
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- name: Crossing Projects
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description: Information about Crossing Projects
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externalDocs:
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description: Docs
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url: https://wiki.brapi.org/
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- name: Crosses
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description: Information about Crosses
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externalDocs:
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description: Docs
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url: https://wiki.brapi.org/
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- name: Seed Lots
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description: Information about Seed Lots
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externalDocs:
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description: Docs
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url: https://wiki.brapi.org/
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- name: Observations
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description: Retrieve and edit information about Observations
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externalDocs:
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description: Docs
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url: https://wiki.brapi.org/
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- name: Observation Units
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description: Retrieve and edit information about Observation Units. An Observation Unit can be anything in a field you might observe as part of a Study
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externalDocs:
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description: Docs
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url: https://wiki.brapi.org/
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- name: Observation Variables
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description: Retrieve and edit information about Observation Variables. An Observation Variable is composed by the unique combination of one Trait, one Method and one Scale.
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externalDocs:
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description: Docs
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url: https://wiki.brapi.org/
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- name: Methods
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description: Retrieve and edit information about Methods.
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externalDocs:
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description: Docs
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url: https://wiki.brapi.org/
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- name: Traits
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description: Retrieve and edit information about Traits.
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externalDocs:
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description: Docs
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url: https://wiki.brapi.org/
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- name: Scales
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description: Retrieve and edit information about Scales.
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externalDocs:
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description: Docs
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url: https://wiki.brapi.org/
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- name: Ontologies
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description: Retrieve and edit information about Ontologies used by a server.
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externalDocs:
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description: Docs
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url: https://wiki.brapi.org/
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- name: Images
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description: Retrieve and edit Images and Image meta-data
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externalDocs:
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description: Docs
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url: https://wiki.brapi.org/
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- name: Events
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description: Retrieve and edit information about Events. Events can be planned like watering or fertilizing, or unplanned like weather or pests.
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externalDocs:
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description: Docs
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url: https://wiki.brapi.org/
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