diff --git a/Specification/BrAPI-Core/Programs/Programs_GET_POST.yaml b/Specification/BrAPI-Core/Programs/Programs_GET_POST.yaml index 08038772..b7d184a9 100644 --- a/Specification/BrAPI-Core/Programs/Programs_GET_POST.yaml +++ b/Specification/BrAPI-Core/Programs/Programs_GET_POST.yaml @@ -8,14 +8,6 @@ paths: summary: Get a filtered list of breeding Programs description: Get a filtered list of breeding Programs. This list can be filtered by common crop name to narrow results to a specific crop. parameters: - - $ref: '#/components/parameters/commonCropName' - - $ref: '#/components/parameters/programDbId' - - name: programName - description: Filter by program name. Exact match. - in: query - required: false - schema: - type: string - name: abbreviation description: Filter by program abbreviation. Exact match. in: query @@ -34,6 +26,9 @@ paths: enum: - STANARD - PROJECT + - $ref: '#/components/parameters/commonCropName' + - $ref: '#/components/parameters/programDbId' + - $ref: '#/components/parameters/programName' - $ref: '#/components/parameters/externalReferenceID' - $ref: '#/components/parameters/externalReferenceId' - $ref: '#/components/parameters/externalReferenceSource' diff --git a/Specification/BrAPI-Core/Studies/Studies_GET_POST.yaml b/Specification/BrAPI-Core/Studies/Studies_GET_POST.yaml index c62e55f9..ea5b6809 100644 --- a/Specification/BrAPI-Core/Studies/Studies_GET_POST.yaml +++ b/Specification/BrAPI-Core/Studies/Studies_GET_POST.yaml @@ -29,24 +29,6 @@ paths: required: false schema: type: string - - description: Filter by trial - in: query - name: trialDbId - required: false - schema: - type: string - - description: Filter by study DbId - in: query - name: studyDbId - required: false - schema: - type: string - - description: Filter by study name - in: query - name: studyName - required: false - schema: - type: string - description: Filter by study code in: query name: studyCode @@ -59,12 +41,6 @@ paths: required: false schema: type: string - - description: Filter by germplasm DbId - in: query - name: germplasmDbId - required: false - schema: - type: string - description: Filter by observation variable DbId in: query name: observationVariableDbId @@ -106,6 +82,10 @@ paths: type: string - $ref: '#/components/parameters/commonCropName' - $ref: '#/components/parameters/programDbId' + - $ref: '#/components/parameters/trialDbId' + - $ref: '#/components/parameters/studyDbId' + - $ref: '#/components/parameters/studyName' + - $ref: '#/components/parameters/germplasmDbId' - $ref: '#/components/parameters/externalReferenceID' - $ref: '#/components/parameters/externalReferenceId' - $ref: '#/components/parameters/externalReferenceSource' diff --git a/Specification/BrAPI-Core/Trials/Trials_GET_POST.yaml b/Specification/BrAPI-Core/Trials/Trials_GET_POST.yaml index c99b2c60..7802f9fb 100644 --- a/Specification/BrAPI-Core/Trials/Trials_GET_POST.yaml +++ b/Specification/BrAPI-Core/Trials/Trials_GET_POST.yaml @@ -62,24 +62,6 @@ paths: schema: type: string format: date - - name: studyDbId - description: Filter by connected studyDbId - in: query - required: false - schema: - type: string - - name: trialDbId - description: Filter by trialDbId - in: query - required: false - schema: - type: string - - name: trialName - description: Filter by trial name - in: query - required: false - schema: - type: string - name: trialPUI description: Filter by trial PUI in: query @@ -111,8 +93,11 @@ paths: - desc - DESC type: string - - $ref: '#/components/parameters/programDbId' - $ref: '#/components/parameters/commonCropName' + - $ref: '#/components/parameters/programDbId' + - $ref: '#/components/parameters/trialDbId' + - $ref: '#/components/parameters/trialName' + - $ref: '#/components/parameters/studyDbId' - $ref: '#/components/parameters/externalReferenceID' - $ref: '#/components/parameters/externalReferenceId' - $ref: '#/components/parameters/externalReferenceSource' diff --git a/Specification/BrAPI-Genotyping/AlleleMatrix/AlleleMatrix_GET.yaml b/Specification/BrAPI-Genotyping/AlleleMatrix/AlleleMatrix_GET.yaml index a72f9015..16bc5ddc 100644 --- a/Specification/BrAPI-Genotyping/AlleleMatrix/AlleleMatrix_GET.yaml +++ b/Specification/BrAPI-Genotyping/AlleleMatrix/AlleleMatrix_GET.yaml @@ -7,7 +7,9 @@ paths: get: summary: Use this endpoint to retrieve a two dimensional matrix of genotype data description: |- - Use this endpoint to retrieve a two dimensional matrix of genotype data. The response structure is based on the VCF format, with the enhanced ability to slice and merge data sets. This allows the user to return the subset of data they are interested in, without having to download the entire genotype file. + Use this endpoint to retrieve a two dimensional matrix of genotype data. The response structure is based on the VCF file format, + but the search and filter parameters give the ability to slice and merge data sets. This allows the user to return the subset of data they are interested in, + without having to download the entire genotype file.
Each row of data (outer array) corresponds to a variant definition, and each column (inner array) corresponds to a callSet. parameters: - name: dimensionVariantPage diff --git a/Specification/BrAPI-Genotyping/AlleleMatrix/GroupDescription.md b/Specification/BrAPI-Genotyping/AlleleMatrix/GroupDescription.md index b47e5dc3..caaab9ae 100644 --- a/Specification/BrAPI-Genotyping/AlleleMatrix/GroupDescription.md +++ b/Specification/BrAPI-Genotyping/AlleleMatrix/GroupDescription.md @@ -1 +1,3 @@ # Group Allele Matrix + +The Allele Matrix object is used to describe a matrix of genotyping results. This 2d array of data reduces the overall size of the response for larger datasets, when compared to the Calls endpoints. This makes genotype data retrieval faster and easier. \ No newline at end of file diff --git a/Specification/BrAPI-Genotyping/AlleleMatrix/Schemas/AlleleMatrix.yaml b/Specification/BrAPI-Genotyping/AlleleMatrix/Schemas/AlleleMatrix.yaml index 06f10b38..ffaddaa7 100644 --- a/Specification/BrAPI-Genotyping/AlleleMatrix/Schemas/AlleleMatrix.yaml +++ b/Specification/BrAPI-Genotyping/AlleleMatrix/Schemas/AlleleMatrix.yaml @@ -89,11 +89,13 @@ components: dataMatrixName: description: |- The name of the field represented in this data matrix. The key word "Genotype" is reserved for the allele matrix. Examples of other metadata matrices include: "Genotype Quality", "Read Depth", and "Haplotype Quality" +
This maps to a FORMAT field in the VCF file standard. type: string example: Genotype dataMatrixAbbreviation: description: |- The abbreviated code of the field represented in this data matrix. These codes should match the VCF standard when possible and the key word "GT" is reserved for the allele matrix. Examples of other metadata matrices include: "GQ", "RD", and "HQ" +
This maps to a FORMAT field in the VCF file standard. type: string example: GT dataMatrix: diff --git a/Specification/BrAPI-Genotyping/AlleleMatrix/Schemas/AlleleMatrixParameters.yaml b/Specification/BrAPI-Genotyping/AlleleMatrix/Schemas/AlleleMatrixParameters.yaml index d2c72292..f9ff84e6 100644 --- a/Specification/BrAPI-Genotyping/AlleleMatrix/Schemas/AlleleMatrixParameters.yaml +++ b/Specification/BrAPI-Genotyping/AlleleMatrix/Schemas/AlleleMatrixParameters.yaml @@ -16,48 +16,48 @@ components: name: preview description: |- Default Value = false -
- If 'preview' is set to true, then the server should only return the lists of 'callSetDbIds', - 'variantDbIds', and 'variantSetDbIds'. The server should not return any matrix data. This - is intended to be a preview and give the client a sense of how large the matrix returned will be -
- If 'preview' is set to false or not set (default), then the server should return all the matrix - data as requested. +
If 'preview' is set to true, then the server should return with the "dataMatrices" field as null or empty. All other data fields should be returned normally. + This is intended to be a preview and give the client a sense of how large the matrix returned will be +
If 'preview' is set to false or not set (default), then the server should return all the matrix data as requested. in: query required: false schema: type: boolean dataMatrixNames: name: dataMatrixNames - description: dataMatrixNames is a comma seperated list of names (ie 'Genotype, Read Depth' etc). This list controls which data matrices are returned in the response. + description: |- + "dataMatrixNames" is a comma seperated list of names (ie 'Genotype, Read Depth' etc). This list controls which data matrices are returned in the response. +
This maps to a FORMAT field in the VCF file standard. in: query required: false schema: type: string dataMatrixAbbreviations: name: dataMatrixAbbreviations - description: dataMatrixAbbreviations is a comma seperated list of abbreviations (ie 'GT, RD' etc). This list controls which data matrices are returned in the response. + description: |- + "dataMatrixAbbreviations" is a comma seperated list of abbreviations (ie 'GT, RD' etc). This list controls which data matrices are returned in the response. +
This maps to a FORMAT field in the VCF file standard. in: query required: false schema: type: string callSetDbId: name: callSetDbId - description: The ID of the `CallSet` to be retrieved. + description: The ID which uniquely identifies a `CallSet` within the given database server in: query required: false schema: type: string variantDbId: name: variantDbId - description: The ID of the `Variant` to be retrieved. + description: The ID which uniquely identifies a `Variant` within the given database server in: query required: false schema: type: string variantSetDbId: name: variantSetDbId - description: The ID of the `VariantSet` to be retrieved. + description: The ID which uniquely identifies a `VariantSet` within the given database server in: query required: false schema: @@ -90,35 +90,14 @@ components: required: false schema: type: string - germplasmPUI: - name: germplasmPUI - description: Permanent unique identifier (DOI, URI, etc.) - in: query - required: false - schema: - type: string - germplasmDbId: - name: germplasmDbId - description: Internal database identifier - in: query - required: false - schema: - type: string - germplasmName: - name: germplasmName - description: Name of the germplasm - in: query - required: false - schema: - type: string positionRange: - name: positionRange - description: |- - The postion range to search -
- Uses the format "contig:start-end" where "contig" is the chromosome or contig name, "start" is - the starting position of the range, and "end" is the ending position of the range - in: query - required: false - schema: - type: string + name: positionRange + description: |- + The postion range to search +
Uses the format "contig:start-end" where "contig" is the chromosome or contig name, "start" is + the starting position of the range, and "end" is the ending position of the range +
Example: CRHOM_1:12000-14000 + in: query + required: false + schema: + type: string diff --git a/Specification/BrAPI-Genotyping/AlleleMatrix/Schemas/AlleleMatrixSearchRequest.yaml b/Specification/BrAPI-Genotyping/AlleleMatrix/Schemas/AlleleMatrixSearchRequest.yaml index fb22df95..abf81f13 100644 --- a/Specification/BrAPI-Genotyping/AlleleMatrix/Schemas/AlleleMatrixSearchRequest.yaml +++ b/Specification/BrAPI-Genotyping/AlleleMatrix/Schemas/AlleleMatrixSearchRequest.yaml @@ -50,13 +50,15 @@ components: default: false example: true dataMatrixNames: - description: dataMatrixNames is a list of names (ie 'Genotype', 'Read Depth' etc). This list controls which data matrices are returned in the response. + description: |- + `dataMatrixNames` is a list of names (ie 'Genotype', 'Read Depth' etc). This list controls which data matrices are returned in the response. type: array items: type: string example: ['Genotype', 'Read Depth'] dataMatrixAbbreviations: - description: dataMatrixAbbreviations is a comma seperated list of abbreviations (ie 'GT', 'RD' etc). This list controls which data matrices are returned in the response. + description: |- + `dataMatrixAbbreviations` is a comma seperated list of abbreviations (ie 'GT', 'RD' etc). This list controls which data matrices are returned in the response. type: array items: type: string @@ -72,43 +74,43 @@ components: type: string example: [ '20:1000-35000', '20:87000-125000' ] germplasmNames: - description: The germplasm to search + description: A list of human readable `Germplasm` names type: array items: type: string example: [ 'a03202ec', '274e4f63' ] germplasmPUIs: - description: The germplasm to search + description: A list of premenant unique identifiers associated with `Germplasm` type: array items: type: string example: [ 'a03202ec', '274e4f63' ] germplasmDbIds: - description: The germplasm to search + description: A list of IDs which uniquely identify `Germplasm` within the given database server type: array items: type: string example: [ 'a03202ec', '274e4f63' ] sampleDbIds: - description: The samples to search + description: A list of IDs which uniquely identify `Samples` within the given database server type: array items: type: string example: [ 'a03202ec', '274e4f63' ] callSetDbIds: - description: The CallSet to search. + description: A list of IDs which uniquely identify `CallSets` within the given database server type: array items: type: string example: [ 'a03202ec', '274e4f63' ] variantDbIds: - description: The Variant to search. + description: A list of IDs which uniquely identify `Variants` within the given database server type: array items: type: string example: [ 'bba0b258', 'ff97d4f0' ] variantSetDbIds: - description: The VariantSet to search. + description: A list of IDs which uniquely identify `VariantSets` within the given database server type: array items: type: string diff --git a/Specification/BrAPI-Genotyping/AlleleMatrix/Search_AlleleMatrix_POST.yaml b/Specification/BrAPI-Genotyping/AlleleMatrix/Search_AlleleMatrix_POST.yaml index 0b3e07e0..fd71bb20 100644 --- a/Specification/BrAPI-Genotyping/AlleleMatrix/Search_AlleleMatrix_POST.yaml +++ b/Specification/BrAPI-Genotyping/AlleleMatrix/Search_AlleleMatrix_POST.yaml @@ -7,7 +7,7 @@ paths: post: summary: Submit a search request for a Allele Matrix description: |- - Use this endpoint to retrieve a two dimensional matrix of genotype data. The response structure is based on the VCF format, with the enhanced ability to slice and merge data sets. This allows the user to return the subset of data they are interested in, without having to download the entire genotype file. + Use this endpoint to retrieve a two dimensional matrix of genotype data. The response structure is based on the VCF format, but the search and filter parameters give the ability to slice and merge data sets. This allows the user to return the subset of data they are interested in, without having to download the entire genotype file.
Each row of data (outer array) corresponds to a variant definition, and each column (inner array) corresponds to a callSet.
Search requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. If a server needs more time to process the request, it might respond with a `searchResultsDbId`. Use the corresponding `GET /search/calls/{searchResultsDbId}` to retrieve the results of the search.
Review the Search Services documentation for additional implementation details. diff --git a/Specification/BrAPI-Genotyping/AlleleMatrix/Search_AlleleMatrix_SearchResultsDbId_GET.yaml b/Specification/BrAPI-Genotyping/AlleleMatrix/Search_AlleleMatrix_SearchResultsDbId_GET.yaml index 4852d4e2..bc1e61f7 100644 --- a/Specification/BrAPI-Genotyping/AlleleMatrix/Search_AlleleMatrix_SearchResultsDbId_GET.yaml +++ b/Specification/BrAPI-Genotyping/AlleleMatrix/Search_AlleleMatrix_SearchResultsDbId_GET.yaml @@ -7,7 +7,7 @@ paths: get: summary: Get the results of a Allele Matrix search request description: |- - Use this endpoint to retrieve a two dimensional matrix of genotype data. The response structure is based on the VCF format, with the enhanced ability to slice and merge data sets. This allows the user to return the subset of data they are interested in, without having to download the entire genotype file. + Use this endpoint to retrieve a two dimensional matrix of genotype data. The response structure is based on the VCF format, but the search and filter parameters give the ability to slice and merge data sets. This allows the user to return the subset of data they are interested in, without having to download the entire genotype file.
Each row of data (outer array) corresponds to a variant definition, and each column (inner array) corresponds to a callSet.
Clients should submit a search request using the corresponding `POST /search/allelematrix` endpoint. Search requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. If a server needs more time to process the request, it might respond with a `searchResultsDbId`. Use this endpoint to retrieve the results of the search.
Review the Search Services documentation for additional implementation details. diff --git a/Specification/BrAPI-Genotyping/CallSets/CallSets_CallSetId_Calls_GET.yaml b/Specification/BrAPI-Genotyping/CallSets/CallSets_CallSetId_Calls_GET.yaml index f95ad884..f41802cd 100644 --- a/Specification/BrAPI-Genotyping/CallSets/CallSets_CallSetId_Calls_GET.yaml +++ b/Specification/BrAPI-Genotyping/CallSets/CallSets_CallSetId_Calls_GET.yaml @@ -10,7 +10,7 @@ paths: Gets a list of `Calls` associated with a `CallSet`. parameters: - name: callSetDbId - description: The ID of the `CallSet` to be retrieved. + description: The ID which uniquely identifies a `CallSet` within the given database server in: path required: true schema: diff --git a/Specification/BrAPI-Genotyping/CallSets/CallSets_CallSetId_GET.yaml b/Specification/BrAPI-Genotyping/CallSets/CallSets_CallSetId_GET.yaml index 98fe1545..0048a0a8 100644 --- a/Specification/BrAPI-Genotyping/CallSets/CallSets_CallSetId_GET.yaml +++ b/Specification/BrAPI-Genotyping/CallSets/CallSets_CallSetId_GET.yaml @@ -9,7 +9,7 @@ paths: description: Gets a `CallSet` by ID. parameters: - name: callSetDbId - description: The ID of the `CallSet` to be retrieved. + description: The ID which uniquely identifies a `CallSet` within the given database server in: path required: true schema: diff --git a/Specification/BrAPI-Genotyping/CallSets/CallSets_GET.yaml b/Specification/BrAPI-Genotyping/CallSets/CallSets_GET.yaml index 336bc384..719c426d 100644 --- a/Specification/BrAPI-Genotyping/CallSets/CallSets_GET.yaml +++ b/Specification/BrAPI-Genotyping/CallSets/CallSets_GET.yaml @@ -8,41 +8,38 @@ paths: summary: Gets a filtered list of `CallSet` JSON objects. description: Gets a filtered list of `CallSet` JSON objects. parameters: - - name: callSetDbId - description: The ID of the `CallSet` to be retrieved. - in: query - required: false - schema: - type: string - - name: callSetName - description: The human readable name of the `CallSet` to be retrieved. - in: query - required: false - schema: - type: string - - name: variantSetDbId - description: The ID of the `VariantSet` to be retrieved. - in: query - required: false - schema: - type: string - - name: sampleDbId - description: The ID of the `VariantSet` to be retrieved. - in: query - required: false - schema: - type: string - - name: germplasmDbId - description: Return only call sets generated from the Sample of this Germplasm - in: query - required: false - schema: - type: string - - $ref: '#/components/parameters/page' - - $ref: '#/components/parameters/pageSize' - - $ref: '#/components/parameters/externalReferenceId' - - $ref: '#/components/parameters/externalReferenceSource' - - $ref: '#/components/parameters/authorizationHeader' + - name: callSetDbId + description: The ID which uniquely identifies a `CallSet` within the given database server + in: query + required: false + schema: + type: string + - name: callSetName + description: The human readable name of a `CallSet`. + in: query + required: false + schema: + type: string + - name: variantSetDbId + description: The ID which uniquely identifies a `VariantSet` within the given database server + in: query + required: false + schema: + type: string + - name: sampleDbId + description: |- + The ID which uniquely identifies a `Sample` within the given database server +
Filter results to only include `CallSets` generated from this `Sample` + in: query + required: false + schema: + type: string + - $ref: '#/components/parameters/germplasmDbId' + - $ref: '#/components/parameters/page' + - $ref: '#/components/parameters/pageSize' + - $ref: '#/components/parameters/externalReferenceId' + - $ref: '#/components/parameters/externalReferenceSource' + - $ref: '#/components/parameters/authorizationHeader' responses: '200': $ref: '#/components/responses/CallSetsListResponse' diff --git a/Specification/BrAPI-Genotyping/CallSets/GroupDescription.md b/Specification/BrAPI-Genotyping/CallSets/GroupDescription.md index 562cf934..ec5c7956 100644 --- a/Specification/BrAPI-Genotyping/CallSets/GroupDescription.md +++ b/Specification/BrAPI-Genotyping/CallSets/GroupDescription.md @@ -1 +1,5 @@ # Group CallSets + +A `CallSet` represents a `Sample` that was used during some sequencing event. In most cases, the `CallSet` will have a 1-to-1 relationship with a given `Sample`. However, in some cases, a single `Sample` may be used in multiple different sequencing events or experiments. The `CallSet` gives an identifier to the relationship between a `Sample` and a genotype sequencing event. + +In a VCF file, `CallSets` are the columns are the data matrix. diff --git a/Specification/BrAPI-Genotyping/CallSets/Schemas/CallSet.yaml b/Specification/BrAPI-Genotyping/CallSets/Schemas/CallSet.yaml index 15bfc734..d4a64724 100644 --- a/Specification/BrAPI-Genotyping/CallSets/Schemas/CallSet.yaml +++ b/Specification/BrAPI-Genotyping/CallSets/Schemas/CallSet.yaml @@ -25,11 +25,11 @@ components: type: string format: date-time callSetDbId: - description: The call set ID. + description: The ID which uniquely identifies a CallSet within the given database server type: string example: eb2bfd3d callSetName: - description: The call set name. + description: The human readable name which identifies a germplasm within the given database server type: string example: Sample_123_DNA_Run_456 updated: @@ -41,7 +41,7 @@ components: type: string example: 708149c1 variantSetDbIds: - description: The IDs of the variant sets this call set has calls in. + description: The IDs of the variantSets this callSet has calls in. items: type: string type: array diff --git a/Specification/BrAPI-Genotyping/CallSets/Schemas/CallSetsSearchRequest.yaml b/Specification/BrAPI-Genotyping/CallSets/Schemas/CallSetsSearchRequest.yaml index 74c99213..2264c6c5 100644 --- a/Specification/BrAPI-Genotyping/CallSets/Schemas/CallSetsSearchRequest.yaml +++ b/Specification/BrAPI-Genotyping/CallSets/Schemas/CallSetsSearchRequest.yaml @@ -17,31 +17,31 @@ components: - type: object properties: sampleDbIds: - description: Return only call sets generated from the provided Biosample IDs. + description: A list of IDs which uniquely identify `Samples` within the given database server type: array items: type: string example: [ '758d3f6d', '39c0a3f7'] sampleNames: - description: Return only call sets generated from the provided Biosample human readable names. + description: A list of human readable names associated with `Samples` type: array items: type: string example: [ 'Sample_123', 'Sample_789' ] callSetDbIds: - description: Only return call sets with these DbIds (case-sensitive, exact match). + description: A list of IDs which uniquely identify `CallSets` within the given database server type: array items: type: string example: [ '6c7486b2', '49c36a73'] callSetNames: - description: Only return call sets with these names (case-sensitive, exact match). + description: A list of human readable names associated with `CallSets` type: array items: type: string example: [ 'Sample_123_DNA_Run_456', 'Sample_789_DNA_Run_101' ] variantSetDbIds: - description: The VariantSet to search. + description: A list of IDs which uniquely identify `VariantSets` within the given database server type: array items: type: string diff --git a/Specification/BrAPI-Genotyping/CallSets/Search_CallSets_POST.yaml b/Specification/BrAPI-Genotyping/CallSets/Search_CallSets_POST.yaml index 90ae448f..9056c927 100644 --- a/Specification/BrAPI-Genotyping/CallSets/Search_CallSets_POST.yaml +++ b/Specification/BrAPI-Genotyping/CallSets/Search_CallSets_POST.yaml @@ -7,11 +7,11 @@ paths: post: summary: Submit a search request for `CallSets` description: |- - Submit a search request for `CallSets`
- Search requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. + Submit a search request for `CallSets` +
Search requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. If a server needs more time to process the request, it might respond with a `searchResultsDbId`. - Use the corresponding `GET /search/callsets/{searchResultsDbId}` to retrieve the results of the search.
- Review the Search Services documentation for additional implementation details. + Use the corresponding `GET /search/callsets/{searchResultsDbId}` to retrieve the results of the search. +
Review the Search Services documentation for additional implementation details. parameters: - $ref: '#/components/parameters/authorizationHeader' requestBody: diff --git a/Specification/BrAPI-Genotyping/CallSets/Search_CallSets_SearchResultsDbId_GET.yaml b/Specification/BrAPI-Genotyping/CallSets/Search_CallSets_SearchResultsDbId_GET.yaml index 8ad5ffd8..e0c2853b 100644 --- a/Specification/BrAPI-Genotyping/CallSets/Search_CallSets_SearchResultsDbId_GET.yaml +++ b/Specification/BrAPI-Genotyping/CallSets/Search_CallSets_SearchResultsDbId_GET.yaml @@ -7,12 +7,12 @@ paths: get: summary: Get the results of a `CallSets` search request description: |- - Get the results of a `CallSets` search request
- Clients should submit a search request using the corresponding `POST /search/callsets` endpoint. + Get the results of a `CallSets` search request +
Clients should submit a search request using the corresponding `POST /search/callsets` endpoint. Search requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. If a server needs more time to process the request, it might respond with a `searchResultsDbId`. - Use this endpoint to retrieve the results of the search.
- Review the Search Services documentation for additional implementation details. + Use this endpoint to retrieve the results of the search. +
Review the Search Services documentation for additional implementation details. parameters: - $ref: '#/components/parameters/searchResultsDbId' - $ref: '#/components/parameters/page' diff --git a/Specification/BrAPI-Genotyping/Calls/Calls_GET_PUT.yaml b/Specification/BrAPI-Genotyping/Calls/Calls_GET_PUT.yaml index c21ccb51..ab5d58a6 100644 --- a/Specification/BrAPI-Genotyping/Calls/Calls_GET_PUT.yaml +++ b/Specification/BrAPI-Genotyping/Calls/Calls_GET_PUT.yaml @@ -10,19 +10,19 @@ paths: Gets a filtered list of `Call` JSON objects. parameters: - name: callSetDbId - description: The ID of the `CallSet` to be retrieved. + description: The ID which uniquely identifies a `CallSet` within the given database server in: query required: false schema: type: string - name: variantDbId - description: The ID of the `Variant` to be retrieved. + description: The ID which uniquely identifies a `Variant` within the given database server in: query required: false schema: type: string - name: variantSetDbId - description: The ID of the `VariantSet` to be retrieved. + description: The ID which uniquely identifies a `VariantSet` within the given database server in: query required: false schema: diff --git a/Specification/BrAPI-Genotyping/Calls/GroupDescription.md b/Specification/BrAPI-Genotyping/Calls/GroupDescription.md index d3d5ebad..4b023d8d 100644 --- a/Specification/BrAPI-Genotyping/Calls/GroupDescription.md +++ b/Specification/BrAPI-Genotyping/Calls/GroupDescription.md @@ -1 +1,5 @@ # Group Calls + +From the GA4GH Variants specification: + +A Call encodes the genotype of an individual with respect to a variant, as determined by some analysis of experimental data. \ No newline at end of file diff --git a/Specification/BrAPI-Genotyping/Calls/Schemas/Call.yaml b/Specification/BrAPI-Genotyping/Calls/Schemas/Call.yaml index 1332b5c6..0902933c 100644 --- a/Specification/BrAPI-Genotyping/Calls/Schemas/Call.yaml +++ b/Specification/BrAPI-Genotyping/Calls/Schemas/Call.yaml @@ -66,11 +66,13 @@ components: fieldName: description: |- The name of the field represented in this Genotype Field. Examples include: "Genotype Quality", "Read Depth", and "Haplotype Quality" +
This maps to a FORMAT field in the VCF file standard. type: string example: Genotype Quality fieldAbbreviation: description: |- The abbreviated code of the field represented in this Genotype Field. These codes should match the VCF standard when possible. Examples include: "GQ", "RD", and "HQ" +
This maps to a FORMAT field in the VCF file standard. type: string example: GQ fieldValue: diff --git a/Specification/BrAPI-Genotyping/Calls/Schemas/CallsSearchRequest.yaml b/Specification/BrAPI-Genotyping/Calls/Schemas/CallsSearchRequest.yaml index 0c7113a7..b554e9bc 100644 --- a/Specification/BrAPI-Genotyping/Calls/Schemas/CallsSearchRequest.yaml +++ b/Specification/BrAPI-Genotyping/Calls/Schemas/CallsSearchRequest.yaml @@ -11,19 +11,19 @@ components: - type: object properties: callSetDbIds: - description: The CallSet to search. + description: A list of IDs which uniquely identify `CallSets` within the given database server type: array items: type: string example: [ 'a03202ec', '274e4f63' ] variantDbIds: - description: The Variant to search. + description: A list of IDs which uniquely identify `Variant` within the given database server type: array items: type: string example: [ 'bba0b258', 'ff97d4f0' ] variantSetDbIds: - description: The VariantSet to search. + description: A list of IDs which uniquely identify `VariantSets` within the given database server type: array items: type: string diff --git a/Specification/BrAPI-Genotyping/GenomeMaps/GroupDescription.md b/Specification/BrAPI-Genotyping/GenomeMaps/GroupDescription.md index 358805a9..7c7d20fd 100644 --- a/Specification/BrAPI-Genotyping/GenomeMaps/GroupDescription.md +++ b/Specification/BrAPI-Genotyping/GenomeMaps/GroupDescription.md @@ -1,7 +1,7 @@ # Group Genome Maps -Retrieving genetic or physical maps +Notes on the `GenomeMaps` objects: - type: [Genetic | Physical] - unit: [cM | Mb] - linkageGroup: may be scaffold (i.e. linkageGroupCount may consist of chromosomes or scaffolds or a combination of the two) diff --git a/Specification/BrAPI-Genotyping/GenomeMaps/Maps_GET.yaml b/Specification/BrAPI-Genotyping/GenomeMaps/Maps_GET.yaml index 0cf07270..5a3a729f 100644 --- a/Specification/BrAPI-Genotyping/GenomeMaps/Maps_GET.yaml +++ b/Specification/BrAPI-Genotyping/GenomeMaps/Maps_GET.yaml @@ -9,13 +9,13 @@ paths: description: Get list of maps parameters: - name: mapDbId - description: The primary DbId for this genomic map + description: The ID which uniquely identifies a `GenomeMap` in: query required: false schema: type: string - name: mapPUI - description: The DOI or other permanent identifier for this genomic map + description: The DOI or other permanent identifier for a `GenomeMap` in: query required: false schema: @@ -27,25 +27,15 @@ paths: schema: type: string - name: type - description: Type of map - in: query - required: false - schema: - type: string - - name: trialDbId - description: Unique Id to filter by Trial - in: query - required: false - schema: - type: string - - name: studyDbId - description: Unique Id to filter by Study + description: The type of map, usually "Genetic" or "Physical" in: query required: false schema: type: string - $ref: '#/components/parameters/commonCropName' - $ref: '#/components/parameters/programDbId' + - $ref: '#/components/parameters/trialDbId' + - $ref: '#/components/parameters/studyDbId' - $ref: '#/components/parameters/page' - $ref: '#/components/parameters/pageSize' - $ref: '#/components/parameters/authorizationHeader' diff --git a/Specification/BrAPI-Genotyping/GenomeMaps/Maps_MapDbId_GET.yaml b/Specification/BrAPI-Genotyping/GenomeMaps/Maps_MapDbId_GET.yaml index 8b2f0bcb..f077d3e5 100644 --- a/Specification/BrAPI-Genotyping/GenomeMaps/Maps_MapDbId_GET.yaml +++ b/Specification/BrAPI-Genotyping/GenomeMaps/Maps_MapDbId_GET.yaml @@ -8,7 +8,7 @@ paths: summary: Get the details of a specific Genomic Map description: Provides the number of markers on each linkageGroup and the max position on the linkageGroup parameters: - - description: The internal db id of a selected map + - description: The ID which uniquely identifies a `GenomeMap` in: path name: mapDbId required: true diff --git a/Specification/BrAPI-Genotyping/GenomeMaps/Maps_MapDbId_LinkageGroups_GET.yaml b/Specification/BrAPI-Genotyping/GenomeMaps/Maps_MapDbId_LinkageGroups_GET.yaml index 4e7c39fd..a43095f8 100644 --- a/Specification/BrAPI-Genotyping/GenomeMaps/Maps_MapDbId_LinkageGroups_GET.yaml +++ b/Specification/BrAPI-Genotyping/GenomeMaps/Maps_MapDbId_LinkageGroups_GET.yaml @@ -8,7 +8,7 @@ paths: summary: Get the Linkage Groups of a specific Genomic Map description: Get the Linkage Groups of a specific Genomic Map. A Linkage Group is the BrAPI generic term for a named section of a map. A Linkage Group can represent a Chromosome, Scaffold, or Linkage Group. parameters: - - description: The internal db id of a selected map + - description: The ID which uniquely identifies a `GenomeMap` in: path name: mapDbId required: true diff --git a/Specification/BrAPI-Genotyping/GenomeMaps/MarkerPositions_GET.yaml b/Specification/BrAPI-Genotyping/GenomeMaps/MarkerPositions_GET.yaml index 23e2564d..90963dac 100644 --- a/Specification/BrAPI-Genotyping/GenomeMaps/MarkerPositions_GET.yaml +++ b/Specification/BrAPI-Genotyping/GenomeMaps/MarkerPositions_GET.yaml @@ -9,13 +9,15 @@ paths: description: Get marker position information, based on Map, Linkage Group, and Marker ID parameters: - name: mapDbId - description: unique id of a map + description: The ID which uniquely identifies a `GenomeMap` in: query required: false schema: type: string - name: linkageGroupName - description: The chromosome identifier or the generic linkage group identifier if the chromosome is not applicable. + description: |- + The Uniquely Identifiable name of a `LinkageGroup` +
This might be a chromosome identifier or the generic linkage group identifier if the chromosome is not applicable. in: query required: false schema: diff --git a/Specification/BrAPI-Genotyping/GenomeMaps/Schemas/GenomeMap.yaml b/Specification/BrAPI-Genotyping/GenomeMaps/Schemas/GenomeMap.yaml index 4a23b2b2..58bb777f 100644 --- a/Specification/BrAPI-Genotyping/GenomeMaps/Schemas/GenomeMap.yaml +++ b/Specification/BrAPI-Genotyping/GenomeMaps/Schemas/GenomeMap.yaml @@ -18,11 +18,11 @@ components: description: Additional arbitrary info type: object comments: - description: Additional comments + description: Additional comments about a `GenomeMap` type: string example: Comments about this map commonCropName: - description: The common name of the crop + description: The common name of the `Crop` type: string example: Paw Paw documentationURL: @@ -31,27 +31,27 @@ components: type: string example: https://brapi.org linkageGroupCount: - description: The number of linkage groups present in this genomic map + description: The number of linkage groups present in a `GenomeMap` type: integer example: 5 mapDbId: - description: The ID which uniquely identifies this genomic map + description: The ID which uniquely identifies a `GenomeMap` type: string example: 142cffd5 mapPUI: - description: The DOI or other permanent identifier for this genomic map + description: The DOI or other permanent identifier for a `GenomeMap` type: string example: doi:10.3207/2959859860 mapName: - description: A human readable name for this genomic map + description: A human readable name for a `GenomeMap` type: string example: Genome Map 1 markerCount: - description: The number of markers present in this genomic map + description: The number of markers present in a `GenomeMap` type: integer example: 1100 publishedDate: - description: The date this genome was published + description: The date this `GenomeMap` was published format: date-time type: string scientificName: @@ -59,11 +59,11 @@ components: type: string example: Zea mays type: - description: The type of map this represents, usually "Genetic" + description: The type of map this represents, usually "Genetic" or "Physical" type: string example: Genetic unit: - description: The units used to describe the data in this map + description: The units used to describe the data in a `GenomeMap` type: string example: cM diff --git a/Specification/BrAPI-Genotyping/GenomeMaps/Schemas/LinkageGroup.yaml b/Specification/BrAPI-Genotyping/GenomeMaps/Schemas/LinkageGroup.yaml index e62c40b6..db95a24a 100644 --- a/Specification/BrAPI-Genotyping/GenomeMaps/Schemas/LinkageGroup.yaml +++ b/Specification/BrAPI-Genotyping/GenomeMaps/Schemas/LinkageGroup.yaml @@ -7,7 +7,7 @@ components: schemas: LinkageGroup: type: object - description: a Linkage Group is the BrAPI generic term for a named section of a map. A Linkage Group can represent a Chromosome, Scaffold, or Linkage Group. + description: a `LinkageGroup` is the generic term for a named section of a `GenomeMap`. A `LinkageGroup` can represent a Chromosome, Scaffold, or Linkage Group. properties: additionalInfo: additionalProperties: @@ -15,14 +15,16 @@ components: description: Additional arbitrary info type: object linkageGroupName: - description: The Uniquely Identifiable name of this linkage group + description: |- + The Uniquely Identifiable name of a `LinkageGroup` +
This might be a chromosome identifier or the generic linkage group identifier if the chromosome is not applicable. type: string example: Chromosome 3 markerCount: - description: The number of markers associated with this linkage group + description: The number of markers associated with a `LinkageGroup` type: integer example: 150 maxPosition: - description: The maximum position of a marker within this linkage group + description: The maximum position of a marker within a `LinkageGroup` type: integer example: 2500 diff --git a/Specification/BrAPI-Genotyping/GenomeMaps/Schemas/MarkerPosition.yaml b/Specification/BrAPI-Genotyping/GenomeMaps/Schemas/MarkerPosition.yaml index 8f012216..bf8b76c0 100644 --- a/Specification/BrAPI-Genotyping/GenomeMaps/Schemas/MarkerPosition.yaml +++ b/Specification/BrAPI-Genotyping/GenomeMaps/Schemas/MarkerPosition.yaml @@ -14,27 +14,33 @@ components: description: Additional arbitrary info type: object mapDbId: - description: The unique ID of the map + description: The ID which uniquely identifies a `GenomeMap` type: string example: 3d52bdf3 mapName: - description: The human readable name of the map + description: A human readable name for a `GenomeMap` type: string example: Genome Map 1 linkageGroupName: - description: The Uniquely Identifiable name of this linkage group + description: |- + The Uniquely Identifiable name of a `LinkageGroup` +
This might be a chromosome identifier or the generic linkage group identifier if the chromosome is not applicable. type: string example: Chromosome 3 position: - description: The position of a marker within a linkage group + description: The position of a marker or variant within a `LinkageGroup` type: integer example: 2390 variantDbId: - description: Internal db identifier + description: |- + The ID which uniquely identifies a `Variant` within the given database server +
A `Variant` can also represent a Marker type: string example: a1eb250a variantName: - description: The human readable name for a marker + description: |- + The human readable name for a `Variant` +
A `Variant` can also represent a Marker type: string example: Marker_2390 diff --git a/Specification/BrAPI-Genotyping/GenomeMaps/Schemas/MarkerPositionSearchRequest.yaml b/Specification/BrAPI-Genotyping/GenomeMaps/Schemas/MarkerPositionSearchRequest.yaml index 295f7f49..0360fc7a 100644 --- a/Specification/BrAPI-Genotyping/GenomeMaps/Schemas/MarkerPositionSearchRequest.yaml +++ b/Specification/BrAPI-Genotyping/GenomeMaps/Schemas/MarkerPositionSearchRequest.yaml @@ -11,29 +11,29 @@ components: - type: object properties: mapDbIds: - description: The unique ID of the map + description: A list of IDs which uniquely identify `GenomeMaps` within the given database server type: array items: type: string example: ['7e6fa8aa', 'bedc418c'] linkageGroupNames: - description: The Uniquely Identifiable name of this linkage group + description: A list of Uniquely Identifiable linkage group names type: array items: type: string example: ['Chromosome 2', 'Chromosome 3'] variantDbIds: - description: Internal db identifier + description: A list of IDs which uniquely identify `Variants` within the given database server type: array items: type: string example: ['a0caa928', 'f8894a26'] minPosition: - description: The minimum position + description: The minimum position of markers in a given map type: integer example: 250 maxPosition: - description: The maximum position + description: The maximum position of markers in a given map type: integer example: 4000 diff --git a/Specification/BrAPI-Genotyping/Plates/GroupDescription.md b/Specification/BrAPI-Genotyping/Plates/GroupDescription.md index 64436f32..a1e84291 100644 --- a/Specification/BrAPI-Genotyping/Plates/GroupDescription.md +++ b/Specification/BrAPI-Genotyping/Plates/GroupDescription.md @@ -1,4 +1,4 @@ # Group Plates -API methods for tracking/managing Plates which contain samples and related meta-data. A 'Plate' is usually a plastic tray full of samples, or a collection of test tubes grouped together. +API methods for tracking/managing `Plates` which contain `Samples` and related meta-data. A `Plate` is usually a plastic tray full of `Samples`, or a collection of test tubes grouped together. diff --git a/Specification/BrAPI-Genotyping/Plates/Plates_GET_POST_PUT.yaml b/Specification/BrAPI-Genotyping/Plates/Plates_GET_POST_PUT.yaml index 3181ae30..42e76222 100644 --- a/Specification/BrAPI-Genotyping/Plates/Plates_GET_POST_PUT.yaml +++ b/Specification/BrAPI-Genotyping/Plates/Plates_GET_POST_PUT.yaml @@ -6,64 +6,49 @@ paths: /plates: get: summary: Get a filtered list of Plates. - description: Get a filtered list of Plates. Each Plate is a collection of samples that are physically grouped together. + description: Get a filtered list of `Plates`. Each `Plate` is a collection of `Samples` that are physically grouped together. parameters: - name: sampleDbId - description: The unique identifier for a Sample + description: The unique identifier for a `Sample` in: query required: false schema: type: string - name: sampleName - description: The human readable name of the sample + description: The human readable name of the `Sample` in: query required: false schema: type: string - name: sampleGroupDbId - description: The unique identifier for a group of related Samples + description: The unique identifier for a group of related `Samples` in: query required: false schema: type: string - name: observationUnitDbId - description: The ID which uniquely identifies an observation unit + description: The ID which uniquely identifies an `ObservationUnit` in: query required: false schema: type: string - name: plateDbId - description: The ID which uniquely identifies a plate of samples + description: The ID which uniquely identifies a `Plate` of `Samples` in: query required: false schema: type: string - name: plateName - description: The human readable name of a plate of samples - in: query - required: false - schema: - type: string - - name: germplasmDbId - description: The ID which uniquely identifies a germplasm - in: query - required: false - schema: - type: string - - name: studyDbId - description: The ID which uniquely identifies a study - in: query - required: false - schema: - type: string - - name: trialDbId - description: The ID which uniquely identifies a trial + description: The human readable name of a `Plate` of `Samples` in: query required: false schema: type: string - $ref: '#/components/parameters/commonCropName' - $ref: '#/components/parameters/programDbId' + - $ref: '#/components/parameters/trialDbId' + - $ref: '#/components/parameters/studyDbId' + - $ref: '#/components/parameters/germplasmDbId' - $ref: '#/components/parameters/externalReferenceID' - $ref: '#/components/parameters/externalReferenceId' - $ref: '#/components/parameters/externalReferenceSource' diff --git a/Specification/BrAPI-Genotyping/Plates/Plates_PlateDbId_GET.yaml b/Specification/BrAPI-Genotyping/Plates/Plates_PlateDbId_GET.yaml index ba2440a0..5db945a9 100644 --- a/Specification/BrAPI-Genotyping/Plates/Plates_PlateDbId_GET.yaml +++ b/Specification/BrAPI-Genotyping/Plates/Plates_PlateDbId_GET.yaml @@ -6,9 +6,9 @@ paths: /plates/{plateDbId}: get: summary: Get the details of a specific Plate. - description: Get the details of a specific Plate. Each Plate is a collection of samples that are physically grouped together. + description: Get the details of a specific `Plate`. Each `Plate` is a collection of `Samples` that are physically grouped together. parameters: - - description: The ID which uniquely identifies a plate + - description: The ID which uniquely identifies a `Plate` in: path name: plateDbId required: true diff --git a/Specification/BrAPI-Genotyping/Plates/Schemas/Plate.yaml b/Specification/BrAPI-Genotyping/Plates/Schemas/Plate.yaml index 657ddbdc..8e6471cd 100644 --- a/Specification/BrAPI-Genotyping/Plates/Schemas/Plate.yaml +++ b/Specification/BrAPI-Genotyping/Plates/Schemas/Plate.yaml @@ -11,8 +11,7 @@ components: - type: object properties: plateDbId: - description: |- - The ID which uniquely identifies a plate + description: The ID which uniquely identifies a `Plate` type: string example: a106467f diff --git a/Specification/BrAPI-Genotyping/Plates/Schemas/PlateNewRequest.yaml b/Specification/BrAPI-Genotyping/Plates/Schemas/PlateNewRequest.yaml index 31111d29..8cea2344 100644 --- a/Specification/BrAPI-Genotyping/Plates/Schemas/PlateNewRequest.yaml +++ b/Specification/BrAPI-Genotyping/Plates/Schemas/PlateNewRequest.yaml @@ -14,11 +14,11 @@ components: description: Additional arbitrary info type: object plateName: - description: A human readable name for a plate + description: A human readable name for a `Plate` type: string example: Plate_123_XYZ plateBarcode: - description: A unique identifier physically attached to the plate + description: A unique identifier physically attached to a `Plate` type: string example: '11223344' sampleType: @@ -31,15 +31,15 @@ components: - MIXED example: TISSUE studyDbId: - description: The ID which uniquely identifies a study within the given database server + description: The ID which uniquely identifies a `Study` within the given database server type: string example: 64bd6bf9 trialDbId: - description: The ID which uniquely identifies a trial within the given database server + description: The ID which uniquely identifies a `Trial` within the given database server type: string example: d34c5349 programDbId: - description: The ID which uniquely identifies a program within the given database server + description: The ID which uniquely identifies a `Program` within the given database server type: string example: bd748e00 plateFormat: diff --git a/Specification/BrAPI-Genotyping/ReferenceSets/GroupDescription.md b/Specification/BrAPI-Genotyping/ReferenceSets/GroupDescription.md index eb42cbd6..c6d64183 100644 --- a/Specification/BrAPI-Genotyping/ReferenceSets/GroupDescription.md +++ b/Specification/BrAPI-Genotyping/ReferenceSets/GroupDescription.md @@ -1 +1,5 @@ # Group Reference Sets + +From GA4GH Variants schema documentation + +A reference genome is a genome assembly that other genomes are compared to and described with respect to. For example, sequencing reads are mapped to and described with respect to a reference genome in the API, and genetic variations are described as edits to reference scaffolds/contigs. In the API a reference genome is described by a ReferenceSet. In turn a ReferenceSet is composed of a set of Reference objects, each which represents a scaffold or contig in the assembly. Reference sequences are expected to have unique names within a ReferenceSet \ No newline at end of file diff --git a/Specification/BrAPI-Genotyping/ReferenceSets/ReferenceSets_GET.yaml b/Specification/BrAPI-Genotyping/ReferenceSets/ReferenceSets_GET.yaml index 3e974881..313875d5 100644 --- a/Specification/BrAPI-Genotyping/ReferenceSets/ReferenceSets_GET.yaml +++ b/Specification/BrAPI-Genotyping/ReferenceSets/ReferenceSets_GET.yaml @@ -28,20 +28,10 @@ paths: in: query schema: type: string - - name: trialDbId - description: The unique identifier for a Trial - in: query - required: false - schema: - type: string - - name: studyDbId - description: The unique identifier for a Study - in: query - required: false - schema: - type: string - $ref: '#/components/parameters/commonCropName' - $ref: '#/components/parameters/programDbId' + - $ref: '#/components/parameters/trialDbId' + - $ref: '#/components/parameters/studyDbId' - $ref: '#/components/parameters/externalReferenceId' - $ref: '#/components/parameters/externalReferenceSource' - $ref: '#/components/parameters/page' diff --git a/Specification/BrAPI-Genotyping/References/GroupDescription.md b/Specification/BrAPI-Genotyping/References/GroupDescription.md index 0216809e..4801ef5f 100644 --- a/Specification/BrAPI-Genotyping/References/GroupDescription.md +++ b/Specification/BrAPI-Genotyping/References/GroupDescription.md @@ -1 +1,5 @@ # Group References + +From GA4GH Variants schema documentation + +A reference genome is a genome assembly that other genomes are compared to and described with respect to. For example, sequencing reads are mapped to and described with respect to a reference genome in the API, and genetic variations are described as edits to reference scaffolds/contigs. In the API a reference genome is described by a ReferenceSet. In turn a ReferenceSet is composed of a set of Reference objects, each which represents a scaffold or contig in the assembly. Reference sequences are expected to have unique names within a ReferenceSet diff --git a/Specification/BrAPI-Genotyping/References/References_GET.yaml b/Specification/BrAPI-Genotyping/References/References_GET.yaml index 3a60121e..c99662e0 100644 --- a/Specification/BrAPI-Genotyping/References/References_GET.yaml +++ b/Specification/BrAPI-Genotyping/References/References_GET.yaml @@ -51,20 +51,10 @@ paths: required: false schema: type: integer - - name: trialDbId - description: The unique identifier for a Trial - in: query - required: false - schema: - type: string - - name: studyDbId - description: The unique identifier for a Study - in: query - required: false - schema: - type: string - $ref: '#/components/parameters/commonCropName' - $ref: '#/components/parameters/programDbId' + - $ref: '#/components/parameters/trialDbId' + - $ref: '#/components/parameters/studyDbId' - $ref: '#/components/parameters/externalReferenceId' - $ref: '#/components/parameters/externalReferenceSource' - $ref: '#/components/parameters/page' diff --git a/Specification/BrAPI-Genotyping/References/Schemas/Reference.yaml b/Specification/BrAPI-Genotyping/References/Schemas/Reference.yaml index 519b2369..9c21d654 100644 --- a/Specification/BrAPI-Genotyping/References/Schemas/Reference.yaml +++ b/Specification/BrAPI-Genotyping/References/Schemas/Reference.yaml @@ -17,19 +17,19 @@ components: externalReferences: $ref: '#/components/schemas/ExternalReferences' referenceDbId: - description: The unique identifier for a Reference + description: The unique identifier for a `Reference` type: string example: fc0a81d0 referenceName: - description: The human readable name of a Reference within a Reference Set. + description: The human readable name of a `Reference` within a `ReferenceSet`. type: string example: Chromosome 2 referenceSetDbId: - description: The unique identifier for a ReferenceSet + description: The unique identifier for a `ReferenceSet` type: string example: c1ecfef1 referenceSetName: - description: The human readable name of a ReferenceSet + description: The human readable name of a `ReferenceSet` type: string example: The Best Assembly Ever isDerived: @@ -38,7 +38,7 @@ components: type: boolean example: false length: - description: The length of this reference's sequence. + description: The length of this `Reference` sequence. type: integer example: 50000000 md5checksum: @@ -52,11 +52,11 @@ components: type: object properties: germplasmDbId: - description: The ID which uniquely identifies a germplasm within the given database server + description: The ID which uniquely identifies a `Germplasm` within the given database server type: string example: d4076594 germplasmName: - description: The human readable name of a germplasm + description: The human readable name of a `Germplasm` type: string example: A0000003 sourceAccessions: @@ -66,7 +66,7 @@ components: type: array example: ["GCF_000001405.26"] sourceDivergence: - description: The `sourceDivergence` is the fraction of non-indel bases that do not match the reference this message was derived from. + description: The `sourceDivergence` is the fraction of non-indel bases that do not match the `Reference` this message was derived from. format: float type: number example: 0.01 diff --git a/Specification/BrAPI-Genotyping/References/Schemas/ReferenceBases.yaml b/Specification/BrAPI-Genotyping/References/Schemas/ReferenceBases.yaml index b03ed5e7..aaf1d65e 100644 --- a/Specification/BrAPI-Genotyping/References/Schemas/ReferenceBases.yaml +++ b/Specification/BrAPI-Genotyping/References/Schemas/ReferenceBases.yaml @@ -6,7 +6,7 @@ paths: {} components: schemas: ReferenceBases: - description: A string representation of the reference base alleles. + description: A string representation of the `Reference` base alleles. type: object properties: nextPageToken: diff --git a/Specification/BrAPI-Genotyping/References/Schemas/ReferencesSearchRequest.yaml b/Specification/BrAPI-Genotyping/References/Schemas/ReferencesSearchRequest.yaml index 7c85f2b9..059bdac3 100644 --- a/Specification/BrAPI-Genotyping/References/Schemas/ReferencesSearchRequest.yaml +++ b/Specification/BrAPI-Genotyping/References/Schemas/ReferencesSearchRequest.yaml @@ -30,13 +30,13 @@ components: example: ['c2365e900c81a89cf74d83dab60df146'] referenceDbIds: type: array - description: The `References` to search. + description: A list of IDs which uniquely identify `References` within the given database server items: type: string example: ['04c83ea7', 'd0998a34'] referenceSetDbIds: type: array - description: The `ReferenceSets` to search. + description: A list of IDs which uniquely identify `ReferenceSets` within the given database server items: type: string example: ['32a19dd7', '2c182c18'] @@ -45,11 +45,11 @@ components: format: boolean type: boolean minLength: - description: The minimum length of this reference's sequence. + description: The minimum length of this `References` sequence. type: integer example: 4000 maxLength: - description: The minimum length of this reference's sequence. + description: The minimum length of this `References` sequence. type: integer example: 90000 diff --git a/Specification/BrAPI-Genotyping/Samples/GroupDescription.md b/Specification/BrAPI-Genotyping/Samples/GroupDescription.md index 9815fd90..3d26006b 100644 --- a/Specification/BrAPI-Genotyping/Samples/GroupDescription.md +++ b/Specification/BrAPI-Genotyping/Samples/GroupDescription.md @@ -1,4 +1,4 @@ # Group Samples -API methods for tracking/managing plant samples and related meta-data. A 'Sample' in the context of BrAPI, is defined as the actual biological plant material collected from the field. +API methods for tracking/managing plant samples and related meta-data. A `Sample`, in the context of BrAPI, is defined as the actual biological plant material collected from the field. diff --git a/Specification/BrAPI-Genotyping/Samples/Samples_GET_POST_PUT.yaml b/Specification/BrAPI-Genotyping/Samples/Samples_GET_POST_PUT.yaml index 895a64cd..83c7acf5 100644 --- a/Specification/BrAPI-Genotyping/Samples/Samples_GET_POST_PUT.yaml +++ b/Specification/BrAPI-Genotyping/Samples/Samples_GET_POST_PUT.yaml @@ -9,61 +9,46 @@ paths: description: Used to retrieve list of Samples from a Sample Tracking system based on some search criteria. parameters: - name: sampleDbId - description: The unique identifier for a Sample + description: The unique identifier for a `Sample` in: query required: false schema: type: string - name: sampleName - description: The human readable name of the sample + description: The human readable name of the `Sample` in: query required: false schema: type: string - name: sampleGroupDbId - description: The unique identifier for a group of related Samples + description: The unique identifier for a group of related `Samples` in: query required: false schema: type: string - name: observationUnitDbId - description: The ID which uniquely identifies an observation unit + description: The ID which uniquely identifies an `ObservationUnit` in: query required: false schema: type: string - name: plateDbId - description: The ID which uniquely identifies a plate of samples + description: The ID which uniquely identifies a `Plate` of `Sample` in: query required: false schema: type: string - name: plateName - description: The human readable name of a plate of samples - in: query - required: false - schema: - type: string - - name: germplasmDbId - description: The ID which uniquely identifies a germplasm - in: query - required: false - schema: - type: string - - name: studyDbId - description: The ID which uniquely identifies a study - in: query - required: false - schema: - type: string - - name: trialDbId - description: The ID which uniquely identifies a trial + description: The human readable name of a `Plate` of `Sample` in: query required: false schema: type: string - $ref: '#/components/parameters/commonCropName' - $ref: '#/components/parameters/programDbId' + - $ref: '#/components/parameters/trialDbId' + - $ref: '#/components/parameters/studyDbId' + - $ref: '#/components/parameters/germplasmDbId' - $ref: '#/components/parameters/externalReferenceID' - $ref: '#/components/parameters/externalReferenceId' - $ref: '#/components/parameters/externalReferenceSource' diff --git a/Specification/BrAPI-Genotyping/Samples/Samples_SampleDbId_GET_PUT.yaml b/Specification/BrAPI-Genotyping/Samples/Samples_SampleDbId_GET_PUT.yaml index 1d5b1e96..661e447d 100644 --- a/Specification/BrAPI-Genotyping/Samples/Samples_SampleDbId_GET_PUT.yaml +++ b/Specification/BrAPI-Genotyping/Samples/Samples_SampleDbId_GET_PUT.yaml @@ -8,7 +8,7 @@ paths: summary: Get the details of a specific Sample description: Used to retrieve the details of a single Sample from a Sample Tracking system. parameters: - - description: the internal DB id for a sample + - description: The unique identifier for a `Sample` in: path name: sampleDbId required: true @@ -35,7 +35,7 @@ paths: **Deprecated in v2.1** Please use `PUT /samples`. Github issue number #462
Update the details of an existing Sample parameters: - - description: the internal DB id for a sample + - description: The unique identifier for a `Sample` in: path name: sampleDbId required: true diff --git a/Specification/BrAPI-Genotyping/Samples/Schemas/Sample.yaml b/Specification/BrAPI-Genotyping/Samples/Schemas/Sample.yaml index 49864df5..18f24b69 100644 --- a/Specification/BrAPI-Genotyping/Samples/Schemas/Sample.yaml +++ b/Specification/BrAPI-Genotyping/Samples/Schemas/Sample.yaml @@ -12,9 +12,8 @@ components: properties: sampleDbId: description: |- - The ID which uniquely identifies a sample - - MIAPPE V1.1 (DM-76) Sample ID - Unique identifier for the sample. + The ID which uniquely identifies a `Sample` +
MIAPPE V1.1 (DM-76) Sample ID - Unique identifier for the sample. type: string example: cd06a61d diff --git a/Specification/BrAPI-Genotyping/Samples/Schemas/SampleNewRequest.yaml b/Specification/BrAPI-Genotyping/Samples/Schemas/SampleNewRequest.yaml index a3af6669..aedb43d3 100644 --- a/Specification/BrAPI-Genotyping/Samples/Schemas/SampleNewRequest.yaml +++ b/Specification/BrAPI-Genotyping/Samples/Schemas/SampleNewRequest.yaml @@ -14,93 +14,89 @@ components: description: Additional arbitrary info type: object germplasmDbId: - description: The ID which uniquely identifies a germplasm + description: The ID which uniquely identifies a `Germplasm` type: string example: 7e08d538 sampleDescription: description: |- - Description of a sample - - MIAPPE V1.1 (DM-79) Sample description - Any information not captured by the other sample fields, including quantification, sample treatments and processing. + Description of a `Sample` +
MIAPPE V1.1 (DM-79) Sample description - Any information not captured by the other sample fields, including quantification, sample treatments and processing. type: string example: This sample was taken from the root of a tree observationUnitDbId: - description: The ID which uniquely identifies an observation unit + description: The ID which uniquely identifies an `ObservationUnit` type: string example: 073a3ce5 plateDbId: - description: The ID which uniquely identifies a plate of samples + description: The ID which uniquely identifies a `Plate` of `Sample` type: string example: 2dce16d1 plateName: - description: The human readable name of a plate + description: The human readable name of a `Plate` type: string example: Plate_alpha_20191022 sampleTimestamp: description: |- - The date and time a sample was collected from the field - - MIAPPE V1.1 (DM-80) Collection date - The date and time when the sample was collected / harvested + The date and time a `Sample` was collected from the field +
MIAPPE V1.1 (DM-80) Collection date - The date and time when the sample was collected / harvested format: date-time type: string sampleName: - description: The human readable name of the sample + description: The human readable name of the `Sample` type: string example: Sample_alpha_20191022 samplePUI: description: |- - A permanent unique identifier for the sample (DOI, URL, UUID, etc) - - MIAPPE V1.1 (DM-81) External ID - An identifier for the sample in a persistent repository, comprising the name of the repository and the accession number of the observation unit therein. Submission to the EBI Biosamples repository is recommended. URI are recommended when possible. + A permanent unique identifier for the `Sample` (DOI, URL, UUID, etc) +
MIAPPE V1.1 (DM-81) External ID - An identifier for the sample in a persistent repository, comprising the name of the repository and the accession number of the observation unit therein. Submission to the EBI Biosamples repository is recommended. URI are recommended when possible. type: string example: doi:10.15454/312953986E3 sampleBarcode: - description: A unique identifier physically attached to the sample + description: A unique identifier physically attached to the `Sample` type: string example: 3a027b59 sampleType: - description: The type of sample taken. ex. 'DNA', 'RNA', 'Tissue', etc + description: The type of `Sample` taken. ex. 'DNA', 'RNA', 'Tissue', etc type: string example: Tissue column: - description: The Column identifier for this samples location in the plate + description: The Column identifier for this `Sample` location in the `Plate` type: integer minimum: 1 maximum: 12 example: 6 row: - description: The Row identifier for this samples location in the plate + description: The Row identifier for this `Sample` location in the `Plate` type: string example: B well: - description: The Well identifier for this samples location in the plate. Usually a concatenation of Row and Column, or just a number if the samples are not part of an ordered plate. + description: The Well identifier for this `Sample` location in the `Plate`. Usually a concatenation of Row and Column, or just a number if the `Samples` are not part of an ordered `Plate`. type: string example: B6 studyDbId: - description: The ID which uniquely identifies a study within the given database server + description: The ID which uniquely identifies a `Study` within the given database server type: string example: 64bd6bf9 trialDbId: - description: The ID which uniquely identifies a trial within the given database server + description: The ID which uniquely identifies a `Trial` within the given database server type: string example: d34c5349 programDbId: - description: The ID which uniquely identifies a program within the given database server + description: The ID which uniquely identifies a `Program` within the given database server type: string example: bd748e00 sampleGroupDbId: - description: The ID which uniquely identifies a group of samples + description: The ID which uniquely identifies a group of `Samples` type: string example: 8524b436 takenBy: - description: The name or identifier of the entity which took the sample from the field + description: The name or identifier of the entity which took the `Sample` from the field type: string example: Bob tissueType: description: |- The type of tissue sampled. ex. 'Leaf', 'Root', etc. - - MIAPPE V1.1 (DM-78) Plant anatomical entity - A description of the plant part (e.g. leaf) or the plant product (e.g. resin) from which the sample was taken, in the form of an accession number to a suitable controlled vocabulary (Plant Ontology). +
MIAPPE V1.1 (DM-78) Plant anatomical entity - A description of the plant part (e.g. leaf) or the plant product (e.g. resin) from which the sample was taken, in the form of an accession number to a suitable controlled vocabulary (Plant Ontology). type: string example: Root externalReferences: diff --git a/Specification/BrAPI-Genotyping/Samples/Schemas/SampleSearchRequest.yaml b/Specification/BrAPI-Genotyping/Samples/Schemas/SampleSearchRequest.yaml index f596fff3..bd0c9a40 100644 --- a/Specification/BrAPI-Genotyping/Samples/Schemas/SampleSearchRequest.yaml +++ b/Specification/BrAPI-Genotyping/Samples/Schemas/SampleSearchRequest.yaml @@ -17,43 +17,43 @@ components: - type: object properties: observationUnitDbIds: - description: The ID which uniquely identifies an observation unit + description: The ID which uniquely identifies an `ObservationUnit` items: type: string type: array example: [ '3cd0ca36', '983f3b14'] plateDbIds: - description: The ID which uniquely identifies a plate of samples + description: The ID which uniquely identifies a `Plate` of `Samples` items: type: string type: array example: [ '0cac98b8', 'b96125fb'] plateNames: - description: The human readable name of a plate of samples + description: The human readable name of a `Plate` of `Samples` items: type: string type: array example: [ '0cac98b8', 'b96125fb'] sampleDbIds: - description: The ID which uniquely identifies a sample + description: The ID which uniquely identifies a `Sample` items: type: string type: array example: [ '3bece2ca', 'dd286cc6'] sampleNames: - description: The human readable name of the sample + description: The human readable name of the `Sample` items: type: string type: array example: [ 'SA_111', 'SA_222'] sampleGroupDbIds: - description: The unique identifier for a group of related Samples + description: The unique identifier for a group of related `Samples` items: type: string type: array example: [ '45e1e2d7', '6cc6dd28'] germplasmDbIds: - description: The ID which uniquely identifies a germplasm + description: The ID which uniquely identifies a `Germplasm` items: type: string type: array diff --git a/Specification/BrAPI-Genotyping/VariantSets/VariantSets_GET.yaml b/Specification/BrAPI-Genotyping/VariantSets/VariantSets_GET.yaml index e9af7410..6dcb3f0f 100644 --- a/Specification/BrAPI-Genotyping/VariantSets/VariantSets_GET.yaml +++ b/Specification/BrAPI-Genotyping/VariantSets/VariantSets_GET.yaml @@ -26,18 +26,6 @@ paths: required: false schema: type: string - - name: studyDbId - description: Filter by study DbId - in: query - required: false - schema: - type: string - - name: studyName - description: Filter by study name - in: query - required: false - schema: - type: string - name: referenceSetDbId description: The ID of the reference set that describes the sequences used by the variants in this set. in: query @@ -46,6 +34,8 @@ paths: type: string - $ref: '#/components/parameters/commonCropName' - $ref: '#/components/parameters/programDbId' + - $ref: '#/components/parameters/studyDbId' + - $ref: '#/components/parameters/studyName' - $ref: '#/components/parameters/externalReferenceId' - $ref: '#/components/parameters/externalReferenceSource' - $ref: '#/components/parameters/page' diff --git a/Specification/BrAPI-Genotyping/Variants/GroupDescription.md b/Specification/BrAPI-Genotyping/Variants/GroupDescription.md index 943a0cbd..01a9440a 100644 --- a/Specification/BrAPI-Genotyping/Variants/GroupDescription.md +++ b/Specification/BrAPI-Genotyping/Variants/GroupDescription.md @@ -1 +1,5 @@ # Group Variants + +A `Variant` describes a site of interest in a genetic sequence. It is usually described in terms of being compared to a `Reference`. + +A `Variant` may also describe a more traditional marker, which can be positioned on a `GenomeMap` diff --git a/Specification/BrAPI-Genotyping/Variants/Schemas/Variant.yaml b/Specification/BrAPI-Genotyping/Variants/Schemas/Variant.yaml index 0dda092d..529e2ace 100644 --- a/Specification/BrAPI-Genotyping/Variants/Schemas/Variant.yaml +++ b/Specification/BrAPI-Genotyping/Variants/Schemas/Variant.yaml @@ -59,8 +59,7 @@ components: end: description: |- This field is optional and may be ignored if there is no relevant map or reference to be associated with. - - The end position (exclusive), resulting in [start, end) closed-open interval. This is typically calculated +
The end position (exclusive), resulting in [start, end) closed-open interval. This is typically calculated by `start + referenceBases.length`. type: integer example: 518 @@ -81,11 +80,11 @@ components: type: boolean example: True variantDbId: - description: The variant ID. + description: The ID which uniquely identifies a `Variant` type: string example: 628e89c5 variantNames: - description: Names for the variant, for example a RefSNP ID. + description: A human readable name associated with a `Variant` items: type: string type: array @@ -113,8 +112,7 @@ components: start: description: |- This field is optional and may be ignored if there is no relevant map or reference to be associated with. - - The start position at which this variant occurs (0-based). This corresponds to the first base of the string +
The start position at which this variant occurs (0-based). This corresponds to the first base of the string of reference bases. Genomic positions are non-negative integers less than reference length. Variants spanning the join of circular genomes are represented as two variants one on each side of the join (position 0). type: integer diff --git a/Specification/BrAPI-Genotyping/Variants/Schemas/VariantsSearchRequest.yaml b/Specification/BrAPI-Genotyping/Variants/Schemas/VariantsSearchRequest.yaml index b35bc157..7b31febb 100644 --- a/Specification/BrAPI-Genotyping/Variants/Schemas/VariantsSearchRequest.yaml +++ b/Specification/BrAPI-Genotyping/Variants/Schemas/VariantsSearchRequest.yaml @@ -36,13 +36,13 @@ components: type: string example: 120a2d5c referenceDbIds: - description: The unique identifier representing a genotype Reference + description: The unique identifier representing a genotype `Reference` items: type: string type: array example: ['89ab4d17', '74d3b63d'] referenceSetDbIds: - description: The unique identifier representing a genotype ReferenceSet + description: The unique identifier representing a genotype `ReferenceSet` items: type: string type: array @@ -52,13 +52,13 @@ components: type: integer example: 100 variantDbIds: - description: The `Variant`s to search. + description: A list of IDs which uniquely identify `Variants` items: type: string type: array example: ['3b63d889', 'ab4d174d'] variantSetDbIds: - description: The `VariantSet` to search. + description: A list of IDs which uniquely identify `VariantSets` items: type: string type: array diff --git a/Specification/BrAPI-Genotyping/Variants/Variants_GET.yaml b/Specification/BrAPI-Genotyping/Variants/Variants_GET.yaml index 2da0dc7e..5f683b07 100644 --- a/Specification/BrAPI-Genotyping/Variants/Variants_GET.yaml +++ b/Specification/BrAPI-Genotyping/Variants/Variants_GET.yaml @@ -10,25 +10,25 @@ paths: Gets a filtered list of `Variants`. parameters: - name: variantDbId - description: The ID of the `Variant` to be retrieved. + description: The ID which uniquely identifies a `Variant` in: query required: false schema: type: string - name: variantSetDbId - description: The ID of the `VariantSet` to be retrieved. + description: The ID which uniquely identifies a `VariantSet` in: query required: false schema: type: string - name: referenceDbId - description: The ID of the `Reference` to be retrieved. + description: The ID which uniquely identifies a `Reference` in: query required: false schema: type: string - name: referenceSetDbId - description: The ID of the `ReferenceSet` to be retrieved. + description: The ID which uniquely identifies a `ReferenceSet` in: query required: false schema: diff --git a/Specification/BrAPI-Genotyping/Variants/Variants_VariantId_Calls_GET.yaml b/Specification/BrAPI-Genotyping/Variants/Variants_VariantId_Calls_GET.yaml index e9b2b364..35046806 100644 --- a/Specification/BrAPI-Genotyping/Variants/Variants_VariantId_Calls_GET.yaml +++ b/Specification/BrAPI-Genotyping/Variants/Variants_VariantId_Calls_GET.yaml @@ -10,7 +10,7 @@ paths: The variant calls for this particular variant. Each one represents the determination of genotype with respect to this variant. `Calls` in this array are implicitly associated with this `Variant`. parameters: - name: variantDbId - description: The ID of the `Variant` to be retrieved. + description: The ID which uniquely identifies a `Variant` in: path required: true schema: diff --git a/Specification/BrAPI-Genotyping/Variants/Variants_VariantId_GET.yaml b/Specification/BrAPI-Genotyping/Variants/Variants_VariantId_GET.yaml index 043cd158..3ede7a52 100644 --- a/Specification/BrAPI-Genotyping/Variants/Variants_VariantId_GET.yaml +++ b/Specification/BrAPI-Genotyping/Variants/Variants_VariantId_GET.yaml @@ -6,10 +6,10 @@ paths: /variants/{variantDbId}: get: summary: Gets a `Variant` by ID. - description: '`GET /variants/{id}` will return a JSON version of `Variant`.' + description: The endpoint `GET /variants/{id}` will return a JSON version of `Variant`. parameters: - name: variantDbId - description: The ID of the `Variant` to be retrieved. + description: The ID which uniquely identifies a `Variant` in: path required: true schema: diff --git a/Specification/BrAPI-Germplasm/Germplasm/Germplasm_GET_POST.yaml b/Specification/BrAPI-Germplasm/Germplasm/Germplasm_GET_POST.yaml index 43900e76..e8e59860 100644 --- a/Specification/BrAPI-Germplasm/Germplasm/Germplasm_GET_POST.yaml +++ b/Specification/BrAPI-Germplasm/Germplasm/Germplasm_GET_POST.yaml @@ -15,24 +15,6 @@ paths: - Possibility to get MCPD details by PUID rather than dbId parameters: - - name: germplasmPUI - description: Permanent unique identifier (DOI, URI, etc.) - in: query - required: false - schema: - type: string - - name: germplasmDbId - description: Internal database identifier - in: query - required: false - schema: - type: string - - name: germplasmName - description: Name of the germplasm - in: query - required: false - schema: - type: string - name: accessionNumber description: Unique identifiers for accessions within a genebank in: query @@ -63,18 +45,6 @@ paths: required: false schema: type: string - - name: trialDbId - description: Search for Germplasm that are associated with a particular Study - in: query - required: false - schema: - type: string - - name: studyDbId - description: Search for Germplasm that are associated with a particular Study - in: query - required: false - schema: - type: string - name: synonym description: Alternative name or ID used to reference this germplasm in: query @@ -95,6 +65,11 @@ paths: type: string - $ref: '#/components/parameters/commonCropName' - $ref: '#/components/parameters/programDbId' + - $ref: '#/components/parameters/trialDbId' + - $ref: '#/components/parameters/studyDbId' + - $ref: '#/components/parameters/germplasmDbId' + - $ref: '#/components/parameters/germplasmName' + - $ref: '#/components/parameters/germplasmPUI' - $ref: '#/components/parameters/externalReferenceID' - $ref: '#/components/parameters/externalReferenceId' - $ref: '#/components/parameters/externalReferenceSource' diff --git a/Specification/BrAPI-Germplasm/Germplasm/Schemas/Germplasm.yaml b/Specification/BrAPI-Germplasm/Germplasm/Schemas/Germplasm.yaml index 3fb953f5..38d31727 100644 --- a/Specification/BrAPI-Germplasm/Germplasm/Schemas/Germplasm.yaml +++ b/Specification/BrAPI-Germplasm/Germplasm/Schemas/Germplasm.yaml @@ -14,8 +14,7 @@ components: properties: germplasmDbId: description: |- - The ID which uniquely identifies a germplasm within the given database server - - MIAPPE V1.1 (DM-41) Biological material ID - Code used to identify the biological material in the data file. Should be unique within the Investigation. Can correspond to experimental plant ID, seed lot ID, etc. This material identification is different from a BiosampleID which corresponds to Observation Unit or Samples sections below. + The ID which uniquely identifies a germplasm within the given database server +
MIAPPE V1.1 (DM-41) Biological material ID - Code used to identify the biological material in the data file. Should be unique within the Investigation. Can correspond to experimental plant ID, seed lot ID, etc. This material identification is different from a BiosampleID which corresponds to Observation Unit or Samples sections below. type: string example: d4076594 \ No newline at end of file diff --git a/Specification/BrAPI-Germplasm/Germplasm_Attribute_Values/AttributesValues_GET_POST.yaml b/Specification/BrAPI-Germplasm/Germplasm_Attribute_Values/AttributesValues_GET_POST.yaml index 39a67e24..05a01e85 100644 --- a/Specification/BrAPI-Germplasm/Germplasm_Attribute_Values/AttributesValues_GET_POST.yaml +++ b/Specification/BrAPI-Germplasm/Germplasm_Attribute_Values/AttributesValues_GET_POST.yaml @@ -26,14 +26,9 @@ paths: required: false schema: type: string - - name: germplasmDbId - description: Get all attributes associated with this germplasm - in: query - required: false - schema: - type: string - $ref: '#/components/parameters/commonCropName' - $ref: '#/components/parameters/programDbId' + - $ref: '#/components/parameters/germplasmDbId' - $ref: '#/components/parameters/externalReferenceID' - $ref: '#/components/parameters/externalReferenceId' - $ref: '#/components/parameters/externalReferenceSource' diff --git a/Specification/BrAPI-Germplasm/Germplasm_Attributes/Attributes_GET_POST.yaml b/Specification/BrAPI-Germplasm/Germplasm_Attributes/Attributes_GET_POST.yaml index 0b25592b..6828d6f1 100644 --- a/Specification/BrAPI-Germplasm/Germplasm_Attributes/Attributes_GET_POST.yaml +++ b/Specification/BrAPI-Germplasm/Germplasm_Attributes/Attributes_GET_POST.yaml @@ -32,12 +32,6 @@ paths: required: false schema: type: string - - name: germplasmDbId - description: Get all attributes associated with this germplasm - in: query - required: false - schema: - type: string - $ref: '#/components/parameters/methodDbId' - $ref: '#/components/parameters/methodName' - $ref: '#/components/parameters/methodPUI' @@ -49,6 +43,7 @@ paths: - $ref: '#/components/parameters/traitPUI' - $ref: '#/components/parameters/commonCropName' - $ref: '#/components/parameters/programDbId' + - $ref: '#/components/parameters/germplasmDbId' - $ref: '#/components/parameters/externalReferenceID' - $ref: '#/components/parameters/externalReferenceId' - $ref: '#/components/parameters/externalReferenceSource' diff --git a/Specification/BrAPI-Germplasm/Pedigree/Pedigree_GET_POST_PUT.yaml b/Specification/BrAPI-Germplasm/Pedigree/Pedigree_GET_POST_PUT.yaml index 1e8078ec..84bf8101 100644 --- a/Specification/BrAPI-Germplasm/Pedigree/Pedigree_GET_POST_PUT.yaml +++ b/Specification/BrAPI-Germplasm/Pedigree/Pedigree_GET_POST_PUT.yaml @@ -8,24 +8,6 @@ paths: summary: Get a filtered list of pedigree nodes which represent a subset of a pedigree tree description: Get a filtered list of pedigree nodes which represent a subset of a pedigree tree parameters: - - name: germplasmPUI - description: The Permanent Unique Identifier (DOI, URI, etc.) for a germplasm - in: query - required: false - schema: - type: string - - name: germplasmDbId - description: The ID which uniquely identifies a germplasm - in: query - required: false - schema: - type: string - - name: germplasmName - description: A human readable name for a germplasm - in: query - required: false - schema: - type: string - name: accessionNumber description: The unique identifier for an accession within a genebank in: query @@ -62,18 +44,6 @@ paths: required: false schema: type: string - - name: trialDbId - description: The ID which uniquely identifies a Trial within the given database server - in: query - required: false - schema: - type: string - - name: studyDbId - description: The ID which uniquely identifies a Study within the given database server - in: query - required: false - schema: - type: string - name: synonym description: An alternative name or ID used to reference this germplasm in: query @@ -118,6 +88,11 @@ paths: type: integer - $ref: '#/components/parameters/commonCropName' - $ref: '#/components/parameters/programDbId' + - $ref: '#/components/parameters/trialDbId' + - $ref: '#/components/parameters/studyDbId' + - $ref: '#/components/parameters/germplasmDbId' + - $ref: '#/components/parameters/germplasmName' + - $ref: '#/components/parameters/germplasmPUI' - $ref: '#/components/parameters/externalReferenceId' - $ref: '#/components/parameters/externalReferenceSource' - $ref: '#/components/parameters/page' diff --git a/Specification/BrAPI-Germplasm/SeedLots/SeedLots_GET_POST.yaml b/Specification/BrAPI-Germplasm/SeedLots/SeedLots_GET_POST.yaml index 8424a726..bcbc7e7f 100644 --- a/Specification/BrAPI-Germplasm/SeedLots/SeedLots_GET_POST.yaml +++ b/Specification/BrAPI-Germplasm/SeedLots/SeedLots_GET_POST.yaml @@ -14,18 +14,6 @@ paths: required: false schema: type: string - - name: germplasmDbId - description: The internal id of the germplasm - in: query - required: false - schema: - type: string - - name: germplasmName - description: Name of the germplasm - in: query - required: false - schema: - type: string - name: crossDbId description: Search for Cross with this unique id in: query @@ -40,6 +28,8 @@ paths: type: string - $ref: '#/components/parameters/commonCropName' - $ref: '#/components/parameters/programDbId' + - $ref: '#/components/parameters/germplasmDbId' + - $ref: '#/components/parameters/germplasmName' - $ref: '#/components/parameters/externalReferenceID' - $ref: '#/components/parameters/externalReferenceId' - $ref: '#/components/parameters/externalReferenceSource' diff --git a/Specification/BrAPI-Germplasm/SeedLots/SeedLots_Transactions_GET_POST.yaml b/Specification/BrAPI-Germplasm/SeedLots/SeedLots_Transactions_GET_POST.yaml index afe5d013..0070a4db 100644 --- a/Specification/BrAPI-Germplasm/SeedLots/SeedLots_Transactions_GET_POST.yaml +++ b/Specification/BrAPI-Germplasm/SeedLots/SeedLots_Transactions_GET_POST.yaml @@ -20,18 +20,6 @@ paths: required: false schema: type: string - - name: germplasmDbId - description: The internal id of the germplasm - in: query - required: false - schema: - type: string - - name: germplasmName - description: Name of the germplasm - in: query - required: false - schema: - type: string - name: crossDbId description: Search for Cross with this unique id in: query @@ -46,6 +34,8 @@ paths: type: string - $ref: '#/components/parameters/commonCropName' - $ref: '#/components/parameters/programDbId' + - $ref: '#/components/parameters/germplasmDbId' + - $ref: '#/components/parameters/germplasmName' - $ref: '#/components/parameters/externalReferenceID' - $ref: '#/components/parameters/externalReferenceId' - $ref: '#/components/parameters/externalReferenceSource' diff --git a/Specification/BrAPI-Phenotyping/Events/Events_GET.yaml b/Specification/BrAPI-Phenotyping/Events/Events_GET.yaml index bc8dc1a3..a4f74d4a 100644 --- a/Specification/BrAPI-Phenotyping/Events/Events_GET.yaml +++ b/Specification/BrAPI-Phenotyping/Events/Events_GET.yaml @@ -8,12 +8,6 @@ paths: summary: Get the Events description: Get list of events parameters: - - description: Filter based on study unique identifier in which the events occurred - in: query - name: studyDbId - required: false - schema: - type: string - description: Filter based on an ObservationUnit unique identifier in which the events occurred in: query name: observationUnitDbId @@ -46,6 +40,7 @@ paths: schema: type: string format: date-time + - $ref: '#/components/parameters/studyDbId' - $ref: '#/components/parameters/page' - $ref: '#/components/parameters/pageSize' - $ref: '#/components/parameters/authorizationHeader' diff --git a/Specification/BrAPI-Phenotyping/ObservationUnits/ObservationLevels_GET.yaml b/Specification/BrAPI-Phenotyping/ObservationUnits/ObservationLevels_GET.yaml index 36253a98..a6dbb2d0 100644 --- a/Specification/BrAPI-Phenotyping/ObservationUnits/ObservationLevels_GET.yaml +++ b/Specification/BrAPI-Phenotyping/ObservationUnits/ObservationLevels_GET.yaml @@ -15,24 +15,9 @@ paths: For more information on Observation Levels, please review the Observation Levels documentation. parameters: - - description: Filter by study DbId - in: query - name: studyDbId - required: false - schema: - type: string - - description: Filter by trial DbId - in: query - name: trialDbId - required: false - schema: - type: string - - description: Filter by program DbId - in: query - name: programDbId - required: false - schema: - type: string + - $ref: '#/components/parameters/programDbId' + - $ref: '#/components/parameters/trialDbId' + - $ref: '#/components/parameters/studyDbId' - $ref: '#/components/parameters/page' - $ref: '#/components/parameters/pageSize' - $ref: '#/components/parameters/authorizationHeader' diff --git a/Specification/BrAPI-Phenotyping/ObservationUnits/ObservationUnits_GET_POST_PUT.yaml b/Specification/BrAPI-Phenotyping/ObservationUnits/ObservationUnits_GET_POST_PUT.yaml index 0415a769..6defa9fa 100644 --- a/Specification/BrAPI-Phenotyping/ObservationUnits/ObservationUnits_GET_POST_PUT.yaml +++ b/Specification/BrAPI-Phenotyping/ObservationUnits/ObservationUnits_GET_POST_PUT.yaml @@ -20,30 +20,12 @@ paths: required: false schema: type: string - - description: The unique ID of a germplasm (accession) to filter on - in: query - name: germplasmDbId - required: false - schema: - type: string - - description: The unique ID of a studies to filter on - in: query - name: studyDbId - required: false - schema: - type: string - description: The unique ID of a location where these observations were collected in: query name: locationDbId required: false schema: type: string - - description: The unique ID of a trial to filter on - in: query - name: trialDbId - required: false - schema: - type: string - description: The year or Phenotyping campaign of a multi-annual study (trees, grape, ...) in: query name: seasonDbId @@ -68,6 +50,9 @@ paths: - $ref: '#/components/parameters/observationUnitLevelRelationshipDbId' - $ref: '#/components/parameters/commonCropName' - $ref: '#/components/parameters/programDbId' + - $ref: '#/components/parameters/trialDbId' + - $ref: '#/components/parameters/studyDbId' + - $ref: '#/components/parameters/germplasmDbId' - $ref: '#/components/parameters/externalReferenceID' - $ref: '#/components/parameters/externalReferenceId' - $ref: '#/components/parameters/externalReferenceSource' diff --git a/Specification/BrAPI-Phenotyping/ObservationUnits/ObservationUnits_Table_GET.yaml b/Specification/BrAPI-Phenotyping/ObservationUnits/ObservationUnits_Table_GET.yaml index 189d6f9d..3df304a0 100644 --- a/Specification/BrAPI-Phenotyping/ObservationUnits/ObservationUnits_Table_GET.yaml +++ b/Specification/BrAPI-Phenotyping/ObservationUnits/ObservationUnits_Table_GET.yaml @@ -50,42 +50,18 @@ paths: required: false schema: type: string - - description: The unique ID of a germplasm (accession) to filter on - in: query - name: germplasmDbId - required: false - schema: - type: string - description: The unique ID of an observation variable in: query name: observationVariableDbId required: false schema: type: string - - description: The unique ID of a studies to filter on - in: query - name: studyDbId - required: false - schema: - type: string - description: The unique ID of a location where these observations were collected in: query name: locationDbId required: false schema: type: string - - description: The unique ID of a trial to filter on - in: query - name: trialDbId - required: false - schema: - type: string - - description: The unique ID of a program to filter on - in: query - name: programDbId - required: false - schema: - type: string - description: The year or Phenotyping campaign of a multi-annual study (trees, grape, ...) in: query name: seasonDbId @@ -101,6 +77,10 @@ paths: schema: type: string deprecated: true + - $ref: '#/components/parameters/programDbId' + - $ref: '#/components/parameters/trialDbId' + - $ref: '#/components/parameters/studyDbId' + - $ref: '#/components/parameters/germplasmDbId' - $ref: '#/components/parameters/observationUnitLevelName' - $ref: '#/components/parameters/observationUnitLevelOrder' - $ref: '#/components/parameters/observationUnitLevelCode' diff --git a/Specification/BrAPI-Phenotyping/Observations/Observations_GET_POST_PUT.yaml b/Specification/BrAPI-Phenotyping/Observations/Observations_GET_POST_PUT.yaml index 928d7ac2..b013b5b7 100644 --- a/Specification/BrAPI-Phenotyping/Observations/Observations_GET_POST_PUT.yaml +++ b/Specification/BrAPI-Phenotyping/Observations/Observations_GET_POST_PUT.yaml @@ -23,36 +23,18 @@ paths: required: false schema: type: string - - description: The unique ID of a germplasm (accession) to filter on - in: query - name: germplasmDbId - required: false - schema: - type: string - description: The unique ID of an observation variable in: query name: observationVariableDbId required: false schema: type: string - - description: The unique ID of a studies to filter on - in: query - name: studyDbId - required: false - schema: - type: string - description: The unique ID of a location where these observations were collected in: query name: locationDbId required: false schema: type: string - - description: The unique ID of a trial to filter on - in: query - name: trialDbId - required: false - schema: - type: string - description: The year or Phenotyping campaign of a multi-annual study (trees, grape, ...) in: query name: seasonDbId @@ -82,6 +64,9 @@ paths: - $ref: '#/components/parameters/observationUnitLevelRelationshipDbId' - $ref: '#/components/parameters/commonCropName' - $ref: '#/components/parameters/programDbId' + - $ref: '#/components/parameters/trialDbId' + - $ref: '#/components/parameters/studyDbId' + - $ref: '#/components/parameters/germplasmDbId' - $ref: '#/components/parameters/externalReferenceID' - $ref: '#/components/parameters/externalReferenceId' - $ref: '#/components/parameters/externalReferenceSource' diff --git a/Specification/BrAPI-Phenotyping/Observations/Observations_Table_GET.yaml b/Specification/BrAPI-Phenotyping/Observations/Observations_Table_GET.yaml index 4a6542ed..2969b2e7 100644 --- a/Specification/BrAPI-Phenotyping/Observations/Observations_Table_GET.yaml +++ b/Specification/BrAPI-Phenotyping/Observations/Observations_Table_GET.yaml @@ -52,42 +52,18 @@ paths: required: false schema: type: string - - description: The unique ID of a germplasm (accession) to filter on - in: query - name: germplasmDbId - required: false - schema: - type: string - description: The unique ID of an observation variable in: query name: observationVariableDbId required: false schema: type: string - - description: The unique ID of a studies to filter on - in: query - name: studyDbId - required: false - schema: - type: string - description: The unique ID of a location where these observations were collected in: query name: locationDbId required: false schema: type: string - - description: The unique ID of a trial to filter on - in: query - name: trialDbId - required: false - schema: - type: string - - description: The unique ID of a program to filter on - in: query - name: programDbId - required: false - schema: - type: string - description: The year or Phenotyping campaign of a multi-annual study (trees, grape, ...) in: query name: seasonDbId @@ -123,6 +99,10 @@ paths: schema: format: date-time type: string + - $ref: '#/components/parameters/programDbId' + - $ref: '#/components/parameters/trialDbId' + - $ref: '#/components/parameters/studyDbId' + - $ref: '#/components/parameters/germplasmDbId' - $ref: '#/components/parameters/observationUnitLevelName' - $ref: '#/components/parameters/observationUnitLevelOrder' - $ref: '#/components/parameters/observationUnitLevelCode' diff --git a/Specification/Components/Parameters/Germplasm.yaml b/Specification/Components/Parameters/Germplasm.yaml new file mode 100644 index 00000000..295dd03a --- /dev/null +++ b/Specification/Components/Parameters/Germplasm.yaml @@ -0,0 +1,34 @@ +info: + title: BrAPI + version: '' +openapi: 3.0.0 +paths: {} +components: + parameters: + germplasmDbId: + name: germplasmDbId + description: |- + Use this parameter to only return results associated with the given `Germplasm` unique identifier. +
Use `GET /germplasm` to find the list of available `Germplasm` on a server. + in: query + required: false + schema: + type: string + germplasmName: + name: germplasmName + description: |- + Use this parameter to only return results associated with the given `Germplasm` by its human readable name. +
Use `GET /germplasm` to find the list of available `Germplasm` on a server. + in: query + required: false + schema: + type: string + germplasmPUI: + name: germplasmPUI + description: |- + Use this parameter to only return results associated with the given `Germplasm` by its global permanent unique identifier. +
Use `GET /germplasm` to find the list of available `Germplasm` on a server. + in: query + required: false + schema: + type: string \ No newline at end of file diff --git a/Specification/Components/Parameters/ProgramTrialStudy.yaml b/Specification/Components/Parameters/ProgramTrialStudy.yaml index e816fee8..9bace3cd 100644 --- a/Specification/Components/Parameters/ProgramTrialStudy.yaml +++ b/Specification/Components/Parameters/ProgramTrialStudy.yaml @@ -8,8 +8,8 @@ components: programDbId: name: programDbId description: |- - Use this parameter to only return results associated with the given Program unique identifier. -
Use `GET /programs` to find the list of available Programs on a server. + Use this parameter to only return results associated with the given `Program` unique identifier. +
Use `GET /programs` to find the list of available `Programs` on a server. in: query required: false schema: @@ -17,8 +17,8 @@ components: programName: name: programName description: |- - Use this parameter to only return results associated with the given Program by its human readable name. -
Use `GET /programs` to find the list of available Programs on a server. + Use this parameter to only return results associated with the given `Program` by its human readable name. +
Use `GET /programs` to find the list of available `Programs` on a server. in: query required: false schema: @@ -26,8 +26,8 @@ components: trialDbId: name: trialDbId description: |- - Use this parameter to only return results associated with the given Trial unique identifier. -
Use `GET /trials` to find the list of available Trials on a server. + Use this parameter to only return results associated with the given `Trial` unique identifier. +
Use `GET /trials` to find the list of available `Trials` on a server. in: query required: false schema: @@ -35,8 +35,8 @@ components: trialName: name: trialName description: |- - Use this parameter to only return results associated with the given Trial by its human readable name. -
Use `GET /trials` to find the list of available Trials on a server. + Use this parameter to only return results associated with the given `Trial` by its human readable name. +
Use `GET /trials` to find the list of available `Trials` on a server. in: query required: false schema: @@ -44,8 +44,8 @@ components: studyDbId: name: studyDbId description: |- - Use this parameter to only return results associated with the given Study unique identifier. -
Use `GET /studies` to find the list of available Studies on a server. + Use this parameter to only return results associated with the given `Study` unique identifier. +
Use `GET /studies` to find the list of available `Studies` on a server. in: query required: false schema: @@ -53,8 +53,8 @@ components: studyName: name: studyName description: |- - Use this parameter to only return results associated with the given Study by its human readable name. -
Use `GET /studies` to find the list of available Studies on a server. + Use this parameter to only return results associated with the given `Study` by its human readable name. +
Use `GET /studies` to find the list of available `Studies` on a server. in: query required: false schema: diff --git a/Specification/Components/Schemas/metadata.yaml b/Specification/Components/Schemas/metadata.yaml index 1b55aec4..0a837677 100644 --- a/Specification/Components/Schemas/metadata.yaml +++ b/Specification/Components/Schemas/metadata.yaml @@ -11,7 +11,14 @@ components: - type: object properties: pagination: - $ref: '#/components/schemas/indexPagination' + $ref: '#/components/schemas/basePagination' + metadataTokenPagination: + allOf: + - $ref: '#/components/schemas/metadataBase' + - type: object + properties: + pagination: + $ref: '#/components/schemas/tokenPagination' metadataBase: type: object properties: @@ -31,18 +38,20 @@ components: items: $ref: '#/components/schemas/status' type: array - metadataTokenPagination: - allOf: - - $ref: '#/components/schemas/metadataBase' - - type: object - properties: - pagination: - $ref: '#/components/schemas/tokenPagination' basePagination: type: object + description: |- + The pagination object is applicable only when the payload contains a "data" key. It describes the pagination of the data contained in the "data" array, as a way to identify which subset of data is being returned. +
Pages are zero indexed, so the first page will be page 0 (zero). required: - pageSize + - currentPage properties: + currentPage: + description: The index number for the returned page of data. This should always match the requested page number or the default page (0). + type: integer + default: 0 + example: 0 pageSize: description: The number of data elements returned, aka the size of the current page. If the requested page does not have enough elements to fill a page at the requested page size, this field should indicate the actual number of elements returned. type: integer @@ -55,31 +64,13 @@ components: totalPages: description: |- The total number of pages of elements available on the server. This should be calculated with the following formula. - - totalPages = CEILING( totalCount / requested_page_size) +
totalPages = CEILING( totalCount / requested_page_size) type: integer example: 1 - indexPagination: - allOf: - - $ref: '#/components/schemas/basePagination' - - type: object - description: |- - The pagination object is applicable only when the payload contains a "data" key. It describes the pagination of the data contained in the "data" array, as a way to identify which subset of data is being returned. - - Pages are zero indexed, so the first page will be page 0 (zero). - required: - - currentPage - properties: - currentPage: - description: The index number for the returned page of data. This should always match the requested page number or the default page (0). - type: integer - default: 0 - example: 0 tokenPagination: allOf: - $ref: '#/components/schemas/basePagination' - type: object - deprecated: true description: |- **Deprecated in v2.1** Please use `page`. Github issue number #451
The pagination object is applicable only when the payload contains a "data" key. It describes the pagination of the data contained in the "data" array, as a way to identify which subset of data is being returned. @@ -108,6 +99,11 @@ components:
The string token used to query the previous page of data. type: string example: 9659857e + example: + currentPage: 0 + pageSize: 1000 + totalCount: 10 + totalPages: 1 dataFile: type: object description: A dataFile contains a URL and the relevant file metadata to represent a file