diff --git a/Specification/BrAPI-Schema/BrAPI-Common/Variable.json b/Specification/BrAPI-Schema/BrAPI-Common/Variable.json index a8bd778a..24c43017 100644 --- a/Specification/BrAPI-Schema/BrAPI-Common/Variable.json +++ b/Specification/BrAPI-Schema/BrAPI-Common/Variable.json @@ -12,7 +12,8 @@ "type": [ "null", "string" - ] + ], + "example": "Maize" }, "contextOfUse": { "description": "Indication of how trait is routinely used. (examples: [\"Trial evaluation\", \"Nursery evaluation\"])", @@ -22,14 +23,16 @@ "type": [ "null", "array" - ] + ], + "example": ["Trial evaluation", "Nursery evaluation"] }, "defaultValue": { "description": "Variable default value. (examples: \"red\", \"2.3\", etc.)", "type": [ "null", "string" - ] + ], + "example": "2.0" }, "documentationURL": { "description": "A URL to the human readable documentation of an object", @@ -37,7 +40,8 @@ "type": [ "null", "string" - ] + ], + "example": "https://wiki.brapi.org/documentation.html" }, "externalReferences": { "description": "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI.", @@ -57,21 +61,24 @@ "type": [ "null", "string" - ] + ], + "example": "flowering" }, "institution": { "description": "Name of institution submitting the variable", "type": [ "null", "string" - ] + ], + "example": "The BrAPI Institute" }, "language": { "description": "2 letter ISO 639-1 code for the language of submission of the variable.", "type": [ "null", "string" - ] + ], + "example": "en" }, "method": { "description": "A description of the way an Observation should be collected. \n
For example, an ObservationVariable might be defined with a Trait of \"plant height\", a Scale of \"meters\", and a Method of \"tape measure\". This variable would be distinct from a variable with the Method \"estimation\" or \"drone image processing\". ", @@ -93,14 +100,16 @@ "type": [ "null", "string" - ] + ], + "example": "Dr. Bob Robertson" }, "status": { "description": "Variable status. (examples: \"recommended\", \"obsolete\", \"legacy\", etc.)", "type": [ "null", "string" - ] + ], + "example": "recommended" }, "submissionTimestamp": { "description": "Timestamp when the Variable was added (ISO 8601)", @@ -118,7 +127,8 @@ "type": [ "null", "array" - ] + ], + "example": ["Maize Height", "Stalk Height", "Corn Height"] }, "trait": { "description": "A Trait describes what property is being observed. \n
For example, an ObservationVariable might be defined with a Trait of \"plant height\", a Scale of \"meters\", and a Method of \"tape measure\". This variable would be distinct from a variable with the Trait \"Leaf length\" or \"Flower height\". ", diff --git a/Specification/BrAPI-Schema/BrAPI-Core/List.json b/Specification/BrAPI-Schema/BrAPI-Core/List.json index 7c58ab0f..6bc5ca7a 100644 --- a/Specification/BrAPI-Schema/BrAPI-Core/List.json +++ b/Specification/BrAPI-Schema/BrAPI-Core/List.json @@ -16,7 +16,8 @@ "type": [ "null", "array" - ] + ], + "example": ["758a78c0", "2c78f9ee"] }, "dateCreated": { "description": "Timestamp when the entity was first created", @@ -56,18 +57,21 @@ "type": [ "null", "string" - ] + ], + "example": "This is a list of germplasm I would like to investigate next season" }, "listName": { "description": "Human readable name of a List", - "type": "string" + "type": "string", + "example": "MyGermplasm_Sept_2020" }, "listOwnerName": { "description": "Human readable name of a List Owner. (usually a user or person)", "type": [ "null", "string" - ] + ], + "example": "Bob Robertson" }, "listOwnerPerson": { "$ref": "Person.json#/$defs/Person", @@ -80,14 +84,16 @@ "type": [ "null", "integer" - ] + ], + "example": 53 }, "listSource": { "description": "The description of where a List originated from", "type": [ "null", "string" - ] + ], + "example": "GeneBank Repository 1.3" }, "listType": { "description": "A flag to indicate the type of objects that are referenced in a List", diff --git a/Specification/BrAPI-Schema/BrAPI-Core/Location.json b/Specification/BrAPI-Schema/BrAPI-Core/Location.json index 81ddcdc2..fcf03673 100644 --- a/Specification/BrAPI-Schema/BrAPI-Core/Location.json +++ b/Specification/BrAPI-Schema/BrAPI-Core/Location.json @@ -7,7 +7,8 @@ "type": [ "null", "string" - ] + ], + "example": "L1" }, "additionalInfo": { "description": "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification.", @@ -19,14 +20,16 @@ "type": [ "null", "string" - ] + ], + "example": "North East corner of greenhouse" }, "coordinateUncertainty": { "description": "Uncertainty associated with the coordinates in meters. Leave the value empty if the uncertainty is unknown.", "type": [ "null", "string" - ] + ], + "example": "20" }, "coordinates": { "description": "One geometry as defined by GeoJSON (RFC 7946). All coordinates are decimal values on the WGS84 geographic coordinate reference system.\n\nCopied from RFC 7946 Section 3.1.1\n\nA position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or\neasting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element.", @@ -38,14 +41,16 @@ "type": [ "null", "string" - ] + ], + "example": "PER" }, "countryName": { "description": "The full name of the country where a Location is located\n
MIAPPE V1.1 (DM-17) Geographic location (country) - The country where the experiment took place, either as a full name or preferably as a 2-letter code.", "type": [ "null", "string" - ] + ], + "example": "Peru" }, "documentationURL": { "description": "A URL to the human readable documentation of an object", @@ -53,21 +58,24 @@ "type": [ "null", "string" - ] + ], + "example": "https://brapi.org" }, "environmentType": { "description": "Describes the general type of environment of a Location. (ex. forest, field, nursery, etc)", "type": [ "null", "string" - ] + ], + "example": "Nursery" }, "exposure": { "description": "Describes the level of protection/exposure for things like sun light and wind at a particular Location", "type": [ "null", "string" - ] + ], + "example": "Structure, no exposure" }, "externalReferences": { "description": "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI.", @@ -87,29 +95,34 @@ "type": [ "null", "string" - ] + ], + "example": "71 Pilgrim Avenue Chevy Chase MD 20815" }, "instituteName": { "description": "The full name of the institute at a particular Location\n
MIAPPE V1.1 (DM-16) Contact institution - Name and address of the institution responsible for the study.", "type": [ "null", "string" - ] + ], + "example": "Plant Science Institute" }, "locationDbId": { "description": "The unique identifier for a Location", - "type": "string" + "type": "string", + "example": "3cfdd67d" }, "locationName": { "description": "A human readable name for a Location\n
MIAPPE V1.1 (DM-18) Experimental site name - The name of the natural site, experimental field, greenhouse, phenotyping facility, etc. where the experiment took place.", - "type": "string" + "type": "string", + "example": "Location 1" }, "locationType": { "description": "A short description of a type of Location (ex. Field Station, Breeding Location, Storage Location, etc)", "type": [ "null", "string" - ] + ], + "example": "Field Station" }, "parentLocation": { "$ref": "Location.json#/$defs/Location", @@ -150,21 +163,24 @@ "type": [ "null", "string" - ] + ], + "example": "Private" }, "slope": { "description": "Describes the approximate slope (height/distance) of a Location.", "type": [ "null", "string" - ] + ], + "example": "0" }, "topography": { "description": "Describes the topography of the land at a Location. (ex. Plateau, Cirque, Hill, Valley, etc)", "type": [ "null", "string" - ] + ], + "example": "Valley" }, "seedLots": { "title": "SeedLots", diff --git a/Specification/BrAPI-Schema/BrAPI-Core/Person.json b/Specification/BrAPI-Schema/BrAPI-Core/Person.json index 929ccdff..f96aa03c 100644 --- a/Specification/BrAPI-Schema/BrAPI-Core/Person.json +++ b/Specification/BrAPI-Schema/BrAPI-Core/Person.json @@ -12,14 +12,16 @@ "type": [ "null", "string" - ] + ], + "example": "Bob likes pina coladas and getting caught in the rain." }, "emailAddress": { "description": "email address for this person", "type": [ "null", "string" - ] + ], + "example": "bob@bob.com" }, "externalReferences": { "description": "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI.", @@ -39,46 +41,53 @@ "type": [ "null", "string" - ] + ], + "example": "Bob" }, "lastName": { "description": "Persons last name", "type": [ "null", "string" - ] + ], + "example": "Robertson" }, "mailingAddress": { "description": "physical address of this person", "type": [ "null", "string" - ] + ], + "example": "123 Street Ave, City, State, Country" }, "middleName": { "description": "Persons middle name", "type": [ "null", "string" - ] + ], + "example": "Danger" }, "personDbId": { "description": "Unique ID for a person", - "type": "string" + "type": "string", + "example": "14340a54" }, "phoneNumber": { "description": "phone number of this person", "type": [ "null", "string" - ] + ], + "example": "+1-555-555-5555" }, "userID": { "description": "A systems user ID associated with this person. Different from personDbId because you could have a person who is not a user of the system.", "type": [ "null", "string" - ] + ], + "example": "bob-23" }, "lists": { "title": "Lists", diff --git a/Specification/BrAPI-Schema/BrAPI-Core/Program.json b/Specification/BrAPI-Schema/BrAPI-Core/Program.json index 99c0877f..ab710c6c 100644 --- a/Specification/BrAPI-Schema/BrAPI-Core/Program.json +++ b/Specification/BrAPI-Schema/BrAPI-Core/Program.json @@ -7,7 +7,8 @@ "type": [ "null", "string" - ] + ], + "example": "P1" }, "additionalInfo": { "description": "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification.", @@ -19,7 +20,8 @@ "type": [ "null", "string" - ] + ], + "example": "Tomatillo" }, "documentationURL": { "description": "A URL to the human readable documentation of an object", @@ -27,7 +29,8 @@ "type": [ "null", "string" - ] + ], + "example": "https://wiki.brapi.org" }, "externalReferences": { "description": "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI.", @@ -47,7 +50,8 @@ "type": [ "null", "string" - ] + ], + "example": "EU: FP7-244374" }, "leadPerson": { "$ref": "Person.json#/$defs/Person", @@ -60,15 +64,18 @@ "type": [ "null", "string" - ] + ], + "example": "Make a better tomatillo" }, "programDbId": { "description": "The ID which uniquely identifies the program", - "type": "string" + "type": "string", + "example": "f60f15b2" }, "programName": { "description": "Human readable name of the program", - "type": "string" + "type": "string", + "example": "Tomatillo_Breeding_Program" }, "programType": { "description": "The type of program entity this object represents\n
'STANDARD' represents a standard, permanent breeding program\n
'PROJECT' represents a short term project, usually with a set time limit based on funding ", @@ -80,7 +87,8 @@ "type": [ "null", "string" - ] + ], + "example": "STANDARD" }, "trials": { "title": "Trials", diff --git a/Specification/BrAPI-Schema/BrAPI-Core/Study.json b/Specification/BrAPI-Schema/BrAPI-Core/Study.json index e366bebf..f035324a 100644 --- a/Specification/BrAPI-Schema/BrAPI-Core/Study.json +++ b/Specification/BrAPI-Schema/BrAPI-Core/Study.json @@ -7,7 +7,8 @@ "type": [ "null", "boolean" - ] + ], + "example": true }, "additionalInfo": { "description": "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification.", @@ -19,7 +20,8 @@ "type": [ "null", "string" - ] + ], + "example": "Grape" }, "contacts": { "description": "List of contact entities associated with this study", @@ -37,7 +39,8 @@ "type": [ "null", "string" - ] + ], + "example": "Irrigation was applied according needs during summer to prevent water stress." }, "dataLinks": { "description": "List of links to extra data files associated with this study. Extra data could include notes, images, and reference data.", @@ -55,7 +58,8 @@ "type": [ "null", "string" - ] + ], + "example": "https://wiki.brapi.org" }, "endDate": { "description": "The date the study ends\n\nMIAPPE V1.1 (DM-15) End date of study - Date and, if relevant, time when the experiment ended", @@ -113,7 +117,8 @@ "type": [ "null", "string" - ] + ], + "example": "MIT License" }, "location": { "$ref": "Location.json#/$defs/Location", @@ -132,6 +137,11 @@ "type": [ "null", "array" + ], + "example": [ + {"levelName": "field", "levelOrder": 0}, + {"levelName": "block", "levelOrder": 1}, + {"levelName": "plot", "levelOrder": 2} ] }, "observationUnitsDescription": { @@ -139,7 +149,8 @@ "type": [ "null", "string" - ] + ], + "example": "Observation units consisted in individual plots themselves consisting of a row of 15 plants at a density of approximately six plants per square meter." }, "observationVariables": { "description": "The list of Observation Variables being used in this study. \n\nThis list is intended to be the wishlist of variables to collect in this study. It may or may not match the set of variables used in the collected observation records. ", @@ -158,7 +169,8 @@ "type": [ "null", "array" - ] + ], + "example": ["Spring_2018"] }, "startDate": { "description": "The date this study started\n\nMIAPPE V1.1 (DM-14) Start date of study - Date and, if relevant, time when the experiment started", @@ -173,36 +185,42 @@ "type": [ "null", "string" - ] + ], + "example": "Grape_Yield_Spring_2018" }, "studyDbId": { "description": "The ID which uniquely identifies a study within the given database server\n\nMIAPPE V1.1 (DM-11) Study unique ID - Unique identifier comprising the name or identifier for the institution/database hosting the submission of the study data, and the identifier of the study in that institution.", - "type": "string" + "type": "string", + "example": "175ac75a" }, "studyDescription": { "description": "The description of this study\n\nMIAPPE V1.1 (DM-13) Study description - Human-readable text describing the study", "type": [ "null", "string" - ] + ], + "example": "This is a yield study for Spring 2018" }, "studyName": { "description": "The human readable name for a study\n\nMIAPPE V1.1 (DM-12) Study title - Human-readable text summarising the study", - "type": "string" + "type": "string", + "example": "INRA's Walnut Genetic Resources Observation at Kenya" }, "studyPUI": { "description": "A permanent unique identifier associated with this study data. For example, a URI or DOI", "type": [ "null", "string" - ] + ], + "example": "doi:10.155454/12349537312" }, "studyType": { "description": "The type of study being performed. ex. \"Yield Trial\", etc", "type": [ "null", "string" - ] + ], + "example": "Phenotyping" }, "trial": { "$ref": "Trial.json#/$defs/Trial", @@ -396,14 +414,16 @@ "type": [ "null", "string" - ] + ], + "example": "CO_715:0000145" }, "description": { "description": "MIAPPE V1.1 (DM-22) Description of the experimental design - Short description of the experimental design, possibly including statistical design. In specific cases, e.g. legacy datasets or data computed from several studies, the experimental design can be \"unknown\"/\"NA\", \"aggregated/reduced data\", or simply 'none'.", "type": [ "null", "string" - ] + ], + "example": "Lines were repeated twice at each location using a complete block design. In order to limit competition effects, each block was organized into four sub-blocks corresponding to earliest groups based on a prior information." }, "study": { "description": "Experimental design associated with a study", @@ -426,14 +446,16 @@ "type": [ "null", "string" - ] + ], + "example": "CO_715:0000162" }, "description": { "description": "MIAPPE V1.1 (DM-26) Description of growth facility - Short description of the facility in which the study was carried out.", "type": [ "null", "string" - ] + ], + "example": "field environment condition, greenhouse" }, "study": { "description": "Growth facility associated with a study", @@ -468,7 +490,8 @@ "type": [ "null", "string" - ] + ], + "example": "1.2.3" }, "study": { "description": "Last update associated with a study", diff --git a/Specification/BrAPI-Schema/BrAPI-Core/Trial.json b/Specification/BrAPI-Schema/BrAPI-Core/Trial.json index 76ae611f..ee0e15de 100644 --- a/Specification/BrAPI-Schema/BrAPI-Core/Trial.json +++ b/Specification/BrAPI-Schema/BrAPI-Core/Trial.json @@ -7,7 +7,8 @@ "type": [ "null", "boolean" - ] + ], + "example": true }, "additionalInfo": { "description": "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification.", @@ -19,7 +20,8 @@ "type": [ "null", "string" - ] + ], + "example": "Wheat" }, "contacts": { "description": "List of contact entities associated with this trial", @@ -52,10 +54,12 @@ "type": [ "null", "string" - ] + ], + "example": "https://wiki.brapi.org" }, "endDate": { "description": "The date this trial ends", + "format": "date", "type": [ "null", "string" @@ -110,6 +114,7 @@ }, "startDate": { "description": "The date this trial started", + "format": "date", "type": [ "null", "string" @@ -117,25 +122,29 @@ }, "trialDbId": { "description": "The ID which uniquely identifies a trial\n\nMIAPPE V1.1 (DM-2) Investigation unique ID - Identifier comprising the unique name of the institution/database hosting the submission of the investigation data, and the accession number of the investigation in that institution.", - "type": "string" + "type": "string", + "example": "1883b402" }, "trialDescription": { "description": "The human readable description of a trial\n\nMIAPPE V1.1 (DM-4) Investigation description - Human-readable text describing the investigation in more detail.", "type": [ "null", "string" - ] + ], + "example": "General drought resistance trial initiated in Peru before duplication in Africa" }, "trialName": { "description": "The human readable name of a trial\n\nMIAPPE V1.1 (DM-3) Investigation title - Human-readable string summarising the investigation.", - "type": "string" + "type": "string", + "example": "Peru Yield Trial 1" }, "trialPUI": { "description": "A permanent identifier for a trial. Could be DOI or other URI formatted identifier.", "type": [ "null", "string" - ] + ], + "example": "https://doi.org/101093190" }, "plates": { "title": "plates", @@ -198,14 +207,16 @@ "type": [ "null", "string" - ] + ], + "example": "doi:10.15454/312953986E3" }, "license": { "description": "MIAPPE V1.1 (DM-7) License - License for the reuse of the data associated with this investigation. The Creative Commons licenses cover most use cases and are recommended.", "type": [ "null", "string" - ] + ], + "example": "https://CreativeCommons.org/licenses/by/4.0" }, "publicReleaseDate": { "description": "MIAPPE V1.1 (DM-6) Public release date - Date of first public release of the dataset presently being described.", @@ -242,14 +253,16 @@ "type": [ "null", "string" - ] + ], + "example": "doi:10.15454/312953986E3" }, "publicationReference": { "description": "The publication reference.", "type": [ "null", "string" - ] + ], + "example": "Selby, BrAPI - An application programming interface for plant breeding applications, Bioinformatics, https://doi.org/10.1093/bioinformatics/190" }, "trial": { "description": "Publications associated with a trial", diff --git a/Specification/BrAPI-Schema/BrAPI-Genotyping/Plate.json b/Specification/BrAPI-Schema/BrAPI-Genotyping/Plate.json index 41512205..76ed1fd9 100644 --- a/Specification/BrAPI-Schema/BrAPI-Genotyping/Plate.json +++ b/Specification/BrAPI-Schema/BrAPI-Genotyping/Plate.json @@ -25,11 +25,13 @@ "type": [ "null", "string" - ] + ], + "example": "11223344" }, "plateDbId": { "description": "The ID which uniquely identifies a `Plate`", - "type": "string" + "type": "string", + "example": "a106467f" }, "plateFormat": { "description": "Enum for plate formats, usually \"PLATE_96\" for a 96 well plate or \"TUBES\" for plateless format", @@ -45,7 +47,8 @@ }, "plateName": { "description": "A human readable name for a `Plate`", - "type": "string" + "type": "string", + "example": "Plate_123_XYZ" }, "program": { "$ref": "../BrAPI-Core/Program.json#/$defs/Program", @@ -65,7 +68,8 @@ "type": [ "null", "string" - ] + ], + "example": "TISSUE" }, "study": { "$ref": "../BrAPI-Core/Study.json#/$defs/Study", diff --git a/Specification/BrAPI-Schema/BrAPI-Genotyping/Sample.json b/Specification/BrAPI-Schema/BrAPI-Genotyping/Sample.json index 408f6d35..c99bec74 100644 --- a/Specification/BrAPI-Schema/BrAPI-Genotyping/Sample.json +++ b/Specification/BrAPI-Schema/BrAPI-Genotyping/Sample.json @@ -28,7 +28,8 @@ "type": [ "null", "integer" - ] + ], + "example": 6 }, "externalReferences": { "description": "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI.", @@ -72,46 +73,50 @@ "type": [ "null", "string" - ] + ], + "example": "B" }, "sampleBarcode": { "description": "A unique identifier physically attached to the `Sample`", "type": [ "null", "string" - ] + ], + "example": "3a027b59" }, "sampleDescription": { "description": "Description of a `Sample`\n
MIAPPE V1.1 (DM-79) Sample description - Any information not captured by the other sample fields, including quantification, sample treatments and processing.", "type": [ "null", "string" - ] + ], + "example": "This sample was taken from the root of a tree" }, "sampleDbId": { "description": "The ID which uniquely identifies a `Sample`\n
MIAPPE V1.1 (DM-76) Sample ID - Unique identifier for the sample.", - "type": [ - "null", - "string" - ] + "type": "string", + "example": "cd06a61d" }, "sampleGroupId": { "description": "The ID which uniquely identifies a group of `Samples`", "type": [ "null", "string" - ] + ], + "example": "8524b436" }, "sampleName": { "description": "The human readable name of the `Sample`", - "type": "string" + "type": "string", + "example": "Sample_alpha_20191022" }, "samplePUI": { "description": "A permanent unique identifier for the `Sample` (DOI, URL, UUID, etc)\n
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": [ "null", "string" - ] + ], + "example": "doi:10.15454/312953986E3" }, "sampleTimestamp": { "description": "The date and time a `Sample` was collected from the field\n
MIAPPE V1.1 (DM-80) Collection date - The date and time when the sample was collected / harvested", @@ -126,7 +131,8 @@ "type": [ "null", "string" - ] + ], + "example": "Tissue" }, "study": { "$ref": "../BrAPI-Core/Study.json#/$defs/Study", @@ -139,14 +145,16 @@ "type": [ "null", "string" - ] + ], + "example": "Bob" }, "tissueType": { "description": "The type of tissue sampled. ex. 'Leaf', 'Root', etc.\n
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": [ "null", "string" - ] + ], + "example": "Root" }, "trial": { "$ref": "../BrAPI-Core/Trial.json#/$defs/Trial", @@ -159,7 +167,8 @@ "type": [ "null", "string" - ] + ], + "example": "B6" } }, "required": [ diff --git a/Specification/BrAPI-Schema/BrAPI-Germplasm/Cross.json b/Specification/BrAPI-Schema/BrAPI-Germplasm/Cross.json index 10b88eb0..7753abbc 100644 --- a/Specification/BrAPI-Schema/BrAPI-Germplasm/Cross.json +++ b/Specification/BrAPI-Schema/BrAPI-Germplasm/Cross.json @@ -23,14 +23,16 @@ }, "crossDbId": { "description": "the unique identifier for a cross", - "type": "string" + "type": "string", + "example": "d105fd6f" }, "crossName": { "description": "the human readable name for a cross", "type": [ "null", "string" - ] + ], + "example": "my_Crosses_2018_01" }, "crossType": { "description": "the type of cross", diff --git a/Specification/BrAPI-Schema/BrAPI-Germplasm/CrossType.json b/Specification/BrAPI-Schema/BrAPI-Germplasm/CrossType.json index a971b749..0d359de9 100644 --- a/Specification/BrAPI-Schema/BrAPI-Germplasm/CrossType.json +++ b/Specification/BrAPI-Schema/BrAPI-Germplasm/CrossType.json @@ -11,7 +11,8 @@ "BULK_OPEN_POLLINATED", "DOUBLE_HAPLOID" ], - "type": "string" + "type": "string", + "example": "BIPARENTAL" } }, "$id": "https://brapi.org/Specification/BrAPI-Schema/BrAPI-Germplasm/CrossType.json", diff --git a/Specification/BrAPI-Schema/BrAPI-Germplasm/CrossingProject.json b/Specification/BrAPI-Schema/BrAPI-Germplasm/CrossingProject.json index b8ad3b7a..01af5245 100644 --- a/Specification/BrAPI-Schema/BrAPI-Germplasm/CrossingProject.json +++ b/Specification/BrAPI-Schema/BrAPI-Germplasm/CrossingProject.json @@ -12,7 +12,8 @@ "type": [ "null", "string" - ] + ], + "example": "Cassava" }, "crossingProjectDbId": { "description": "The unique identifier for a crossing project", @@ -23,11 +24,13 @@ "type": [ "null", "string" - ] + ], + "example": "Crosses between germplasm X and germplasm Y in male nursery study X_2018 and female nursery study Y_2018" }, "crossingProjectName": { "description": "The human readable name for a crossing project", - "type": "string" + "type": "string", + "example": "Crosses_2018" }, "externalReferences": { "description": "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI.", diff --git a/Specification/BrAPI-Schema/BrAPI-Germplasm/Germplasm.json b/Specification/BrAPI-Schema/BrAPI-Germplasm/Germplasm.json index 52874487..828b7e86 100644 --- a/Specification/BrAPI-Schema/BrAPI-Germplasm/Germplasm.json +++ b/Specification/BrAPI-Schema/BrAPI-Germplasm/Germplasm.json @@ -7,7 +7,8 @@ "type": [ "null", "string" - ] + ], + "example": "A0000003" }, "acquisitionDate": { "description": "The date a material or germplasm was acquired by the genebank \n\nMCPD (v2.1) (ACQDATE) 12. Date on which the accession entered the collection [YYYYMMDD] where YYYY is the year, MM is the month and DD is the day. Missing data (MM or DD) should be indicated with hyphens or \"00\" [double zero].", @@ -50,14 +51,16 @@ "type": [ "null", "string" - ] + ], + "example": "420" }, "biologicalStatusOfAccessionDescription": { "description": "Supplemental text description for 'biologicalStatusOfAccessionCode'", "type": [ "null", "string" - ] + ], + "example": "Genetic stock" }, "breedingMethod": { "$ref": "BreedingMethod.json#/$defs/BreedingMethod", @@ -70,25 +73,29 @@ "type": [ "null", "string" - ] + ], + "example": "Rice Diversity Panel 1 (RDP1)" }, "commonCropName": { "description": "Common name for the crop \n\nMCPD (v2.1) (CROPNAME) 10. Common name of the crop. Example: \"malting barley\", \"mas\".", - "type": "string" + "type": "string", + "example": "Maize" }, "countryOfOriginCode": { "description": "3-letter ISO 3166-1 code of the country in which the sample was originally collected \n\nMCPD (v2.1) (ORIGCTY) 13. 3-letter ISO 3166-1 code of the country in which the sample was originally collected (e.g. landrace, crop wild relative, farmers variety), bred or selected (breeding lines, GMOs, segregating populations, hybrids, modern cultivars, etc.). Note- Descriptors 14 to 16 below should be completed accordingly only if it was \"collected\".", "type": [ "null", "string" - ] + ], + "example": "BES" }, "defaultDisplayName": { "description": "Human readable name used for display purposes", "type": [ "null", "string" - ] + ], + "example": "A0000003" }, "documentationURL": { "description": "A URL to the human readable documentation of an object", @@ -96,7 +103,8 @@ "type": [ "null", "string" - ] + ], + "example": "https://wiki.brapi.org" }, "donors": { "description": "List of donor institutes", @@ -130,15 +138,18 @@ "type": [ "null", "string" - ] + ], + "example": "Aspergillus" }, "germplasmDbId": { "description": "The ID which uniquely identifies a germplasm within the given database server \n
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, inventory lot ID, etc. This material identification is different from a BiosampleID which corresponds to Observation Unit or Samples sections below.", - "type": "string" + "type": "string", + "example": "d4076594" }, "germplasmName": { "description": "Name of the germplasm. It can be the preferred name and does not have to be unique.\n\nMCPD (v2.1) (ACCENAME) 11. Either a registered or other designation given to the material received, other than the donors accession number (23) or collecting number (3). First letter uppercase. Multiple names are separated by a semicolon without space.", - "type": "string" + "type": "string", + "example": "A0000003" }, "germplasmOrigin": { "description": "Information for material (orchard, natural sites, ...). Geographic identification of the plants from which seeds or cutting have been taken to produce that germplasm.", @@ -156,63 +167,72 @@ }, "germplasmPUI": { "description": "The Permanent Unique Identifier which represents a germplasm\n\nMIAPPE 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, inventory lot ID, etc This material identification is different from a BiosampleID which corresponds to Observation Unit or Samples sections below.\n\nMIAPPE V1.1 (DM-51) Material source DOI - Digital Object Identifier (DOI) of the material source\n\nMCPD (v2.1) (PUID) 0. Any persistent, unique identifier assigned to the accession so it can be unambiguously referenced at the global level and the information associated with it harvested through automated means. Report one PUID for each accession. The Secretariat of the International Treaty on Plant Genetic Resources for Food and Agriculture (PGRFA) is facilitating the assignment of a persistent unique identifier (PUID), in the form of a DOI, to PGRFA at the accession level. Genebanks not applying a true PUID to their accessions should use, and request recipients to use, the concatenation of INSTCODE, ACCENUMB, and GENUS as a globally unique identifier similar in most respects to the PUID whenever they exchange information on accessions with third parties.", - "type": "string" + "type": "string", + "example": "http://pui.per/accession/A0000003" }, "germplasmPreprocessing": { "description": "Description of any process or treatment applied uniformly to the germplasm, prior to the study itself. Can be provided as free text or as an accession number from a suitable controlled vocabulary.", "type": [ "null", "string" - ] + ], + "example": "EO:0007210; transplanted from study 2351 observation unit ID: pot:894" }, "instituteCode": { "description": "The code for the institute that maintains the material. \n\nMCPD (v2.1) (INSTCODE) 1. FAO WIEWS code of the institute where the accession is maintained. The codes consist of the 3-letter ISO 3166 country code of the country where the institute is located plus a number (e.g. PER001). The current set of institute codes is available from http://www.fao.org/wiews. For those institutes not yet having an FAO Code, or for those with \"obsolete\" codes, see \"Common formatting rules (v)\".", "type": [ "null", "string" - ] + ], + "example": "PER001" }, "instituteName": { "description": "The name of the institute that maintains the material", "type": [ "null", "string" - ] + ], + "example": "The BrAPI Institute" }, "pedigree": { "description": "The cross name and optional selection history.\n\nMCPD (v2.1) (ANCEST) 20. Information about either pedigree or other description of ancestral information (e.g. parent variety in case of mutant or selection). For example a pedigree 'Hanna/7*Atlas//Turk/8*Atlas' or a description 'mutation found in Hanna', 'selection from Irene' or 'cross involving amongst others Hanna and Irene'.", "type": [ "null", "string" - ] + ], + "example": "A0000001/A0000002" }, "seedSource": { "description": "An identifier for the source of the biological material\n
MIAPPE V1.1 (DM-50) Material source ID (Holding institute/stock centre, accession) - An identifier for the source of the biological material, in the form of a key-value pair comprising the name/identifier of the repository from which the material was sourced plus the accession number of the repository for that material. Where an accession number has not been assigned, but the material has been derived from the crossing of known accessions, the material can be defined as follows: \"mother_accession X father_accession\", or, if father is unknown, as \"mother_accession X UNKNOWN\". For in situ material, the region of provenance may be used when an accession is not available.", "type": [ "null", "string" - ] + ], + "example": "INRA:095115_inra" }, "seedSourceDescription": { "description": "Description of the material source\n\nMIAPPE V1.1 (DM-56) Material source description - Description of the material source", "type": [ "null", "string" - ] + ], + "example": "Branches were collected from a 10-year-old tree growing in a progeny trial established in a loamy brown earth soil." }, "species": { "description": "Specific epithet portion of the scientific name in lowercase letters.\n\nMCPD (v2.1) (SPECIES) 6. Specific epithet portion of the scientific name in lowercase letters. Only the following abbreviation is allowed: \"sp.\" \n\nMIAPPE V1.1 (DM-44) Species - Species name (formally: specific epithet) for the organism under study, according to standard scientific nomenclature.", "type": [ "null", "string" - ] + ], + "example": "fructus" }, "speciesAuthority": { "description": "The authority organization responsible for tracking and maintaining the species name \n\nMCPD (v2.1) (SPAUTHOR) 7. Provide the authority for the species name.", "type": [ "null", "string" - ] + ], + "example": "Smith, 1822" }, "storageTypes": { "description": "The type of storage this germplasm is kept in at a genebank.", @@ -233,14 +253,16 @@ "type": [ "null", "string" - ] + ], + "example": "Aspergillus fructus A" }, "subtaxaAuthority": { "description": "The authority organization responsible for tracking and maintaining the subtaxon information\n\nMCPD (v2.1) (SUBTAUTHOR) 9. Provide the subtaxon authority at the most detailed taxonomic level.", "type": [ "null", "string" - ] + ], + "example": "Smith, 1822" }, "synonyms": { "description": "List of alternative names or IDs used to reference this germplasm\n\nMCPD (v2.1) (OTHERNUMB) 24. Any other identifiers known to exist in other collections for this accession. Use the following format: INSTCODE:ACCENUMB;INSTCODE:identifier;INSTCODE and identifier are separated by a colon without space. Pairs of INSTCODE and identifier are separated by a semicolon without space. When the institute is not known, the identifier should be preceded by a colon.", diff --git a/Specification/BrAPI-Schema/BrAPI-Germplasm/GermplasmAttributeValue.json b/Specification/BrAPI-Schema/BrAPI-Germplasm/GermplasmAttributeValue.json index c5ba60cf..9d0e75de 100644 --- a/Specification/BrAPI-Schema/BrAPI-Germplasm/GermplasmAttributeValue.json +++ b/Specification/BrAPI-Schema/BrAPI-Germplasm/GermplasmAttributeValue.json @@ -49,7 +49,8 @@ "type": [ "null", "string" - ] + ], + "example": "Present" } }, "required": [ diff --git a/Specification/BrAPI-Schema/BrAPI-Germplasm/PlannedCross.json b/Specification/BrAPI-Schema/BrAPI-Germplasm/PlannedCross.json index 900996ce..72c5a418 100644 --- a/Specification/BrAPI-Schema/BrAPI-Germplasm/PlannedCross.json +++ b/Specification/BrAPI-Schema/BrAPI-Germplasm/PlannedCross.json @@ -9,7 +9,8 @@ }, "crossType": { "description": "the type of cross", - "$ref": "CrossType.json#/$defs/CrossType" + "$ref": "CrossType.json#/$defs/CrossType", + "example": "BIPARENTAL" }, "crossingProject": { "$ref": "CrossingProject.json#/$defs/CrossingProject", @@ -47,7 +48,8 @@ "type": [ "null", "string" - ] + ], + "example": "my_Crosses_2018_01" }, "status": { "description": "The status of this planned cross. Is it waiting to be performed ('TODO'), has it been completed successfully ('DONE'), or has it not been done on purpose ('SKIPPED').", @@ -61,7 +63,8 @@ "null", "string" ], - "title": "PlannedCrossStatus" + "title": "PlannedCrossStatus", + "example": "TODO" }, "crosses": { "title": "crosses", diff --git a/Specification/BrAPI-Schema/BrAPI-Germplasm/SeedLot.json b/Specification/BrAPI-Schema/BrAPI-Germplasm/SeedLot.json index c3159b0a..586657ee 100644 --- a/Specification/BrAPI-Schema/BrAPI-Germplasm/SeedLot.json +++ b/Specification/BrAPI-Schema/BrAPI-Germplasm/SeedLot.json @@ -12,7 +12,8 @@ "type": [ "null", "number" - ] + ], + "example": 561 }, "contentMixture": { "description": "The mixture of germplasm present in the seed lot.\n
\nIf this seed lot only contains a single germplasm, the response should contain the name \nand DbId of that germplasm with a mixturePercentage value of 100\n
\nIf the seed lot contains a mixture of different germplasm, the response should contain \nthe name and DbId every germplasm present. The mixturePercentage field should contain \nthe ratio of each germplasm in the total mixture. All of the mixturePercentage values \nin this array should sum to equal 100.", @@ -71,39 +72,45 @@ }, "seedLotDbId": { "description": "Unique DbId for the Seed Lot", - "type": "string" + "type": "string", + "example": "261ecb09" }, "seedLotDescription": { "description": "A general description of this Seed Lot", "type": [ "null", "string" - ] + ], + "example": "This is a description of a seed lot" }, "seedLotName": { "description": "A human readable name for this Seed Lot", - "type": "string" + "type": "string", + "example": "Seed Lot Alpha" }, "sourceCollection": { "description": "The description of the source where this material was originally collected (wild, nursery, etc)", "type": [ "null", "string" - ] + ], + "example": "nursery" }, "storageLocation": { "description": "Description the storage location", "type": [ "null", "string" - ] + ], + "example": "The storage location is an massive, underground, bunker." }, "units": { "description": "A description of the things being counted in a SeedLot (seeds, bulbs, kg, tree, etc)", "type": [ "null", "string" - ] + ], + "example": "seeds" }, "fromSeedLotTransactions": { "title": "fromSeedLotTransactions", diff --git a/Specification/BrAPI-Schema/BrAPI-Germplasm/SeedLotTransaction.json b/Specification/BrAPI-Schema/BrAPI-Germplasm/SeedLotTransaction.json index 260115cb..c3669fb1 100644 --- a/Specification/BrAPI-Schema/BrAPI-Germplasm/SeedLotTransaction.json +++ b/Specification/BrAPI-Schema/BrAPI-Germplasm/SeedLotTransaction.json @@ -12,7 +12,8 @@ "type": [ "null", "number" - ] + ], + "example": 45 }, "externalReferences": { "description": "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI.", @@ -48,7 +49,8 @@ "type": [ "null", "string" - ] + ], + "example": "f9cd88d2" }, "transactionTimestamp": { "description": "The time stamp for when the transaction occurred", @@ -63,7 +65,8 @@ "type": [ "null", "string" - ] + ], + "example": "seeds" } }, "required": [ diff --git a/Specification/BrAPI-Schema/BrAPI-Phenotyping/Image.json b/Specification/BrAPI-Schema/BrAPI-Phenotyping/Image.json index 9eb5683e..fbd778d4 100644 --- a/Specification/BrAPI-Schema/BrAPI-Phenotyping/Image.json +++ b/Specification/BrAPI-Schema/BrAPI-Phenotyping/Image.json @@ -11,14 +11,16 @@ "type": [ "null", "string" - ] + ], + "example": "Copyright 2018 Bob Robertson" }, "description": { "description": "The human readable description of an image.", "type": [ "null", "string" - ] + ], + "example": "This is a picture of a tomato" }, "descriptiveOntologyTerms": { "description": "A list of terms to formally describe the image. Each item could be a simple Tag, an Ontology reference Id, or a full ontology URL.", @@ -28,7 +30,8 @@ "type": [ "null", "array" - ] + ], + "example": ["doi:10.1002/0470841559", "Red", "ncbi:0300294"] }, "externalReferences": { "description": "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI.", @@ -52,21 +55,24 @@ "type": [ "null", "string" - ] + ], + "example": "image_0000231.jpg" }, "imageFileSize": { "description": "The size of the image in Bytes.", "type": [ "null", "integer" - ] + ], + "example": 50000 }, "imageHeight": { "description": "The height of the image in Pixels.", "type": [ "null", "integer" - ] + ], + "example": 550 }, "imageLocation": { "description": "One geometry as defined by GeoJSON (RFC 7946). All coordinates are decimal values on the WGS84 geographic coordinate reference system.\n\nCopied from RFC 7946 Section 3.1.1\n\nA position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or\neasting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element.", @@ -79,7 +85,8 @@ "type": [ "null", "string" - ] + ], + "example": "Tomato Image 1" }, "imageTimeStamp": { "description": "The date and time the image was taken", @@ -94,14 +101,16 @@ "type": [ "null", "string" - ] + ], + "example": "https://wiki.brapi.org/images/tomato" }, "imageWidth": { "description": "The width of the image in Pixels.", "type": [ "null", "integer" - ] + ], + "example": 700 }, "mimeType": { "description": "The file type of the image. Examples 'image/jpeg', 'image/png', 'image/svg', etc", @@ -109,7 +118,8 @@ "type": [ "null", "string" - ] + ], + "example": "image/jpeg" }, "observationUnit": { "$ref": "ObservationUnit.json#/$defs/ObservationUnit", diff --git a/Specification/BrAPI-Schema/BrAPI-Phenotyping/Method.json b/Specification/BrAPI-Schema/BrAPI-Phenotyping/Method.json index 12b70fb7..6f80c1a1 100644 --- a/Specification/BrAPI-Schema/BrAPI-Phenotyping/Method.json +++ b/Specification/BrAPI-Schema/BrAPI-Phenotyping/Method.json @@ -12,14 +12,16 @@ "type": [ "null", "string" - ] + ], + "example": "Smith, 1893, Really Cool Paper, Popular Journal" }, "description": { "description": "Method description\n
MIAPPE V1.1 (DM-90) Method description - Textual description of the method, which may extend a method defined in an external reference with specific parameters, e.g. growth stage, inoculation precise organ (leaf number)", "type": [ "null", "string" - ] + ], + "example": "A measuring tape was used" }, "externalReferences": { "description": "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI.", @@ -39,14 +41,16 @@ "type": [ "null", "string" - ] + ], + "example": "a^2 + b^2 = c^2" }, "methodClass": { "description": "Method class (examples: \"Measurement\", \"Counting\", \"Estimation\", \"Computation\", etc.)", "type": [ "null", "string" - ] + ], + "example": "Measurement" }, "methodDbId": { "description": "Method unique identifier", @@ -57,14 +61,16 @@ }, "methodName": { "description": "Human readable name for the method\n
MIAPPE V1.1 (DM-88) Method Name of the method of observation", - "type": "string" + "type": "string", + "example": "Measuring Tape" }, "methodPUI": { "description": "The Permanent Unique Identifier of a Method, usually in the form of a URI", "type": [ "null", "string" - ] + ], + "example": "http://my-traits.com/trait/CO_123:0000212" }, "ontologyReference": { "description": "MIAPPE V1.1\n\n(DM-85) Variable accession number - Accession number of the variable in the Crop Ontology\n\n(DM-87) Trait accession number - Accession number of the trait in a suitable controlled vocabulary (Crop Ontology, Trait Ontology).\n\n(DM-89) Method accession number - Accession number of the method in a suitable controlled vocabulary (Crop Ontology, Trait Ontology).\n\n(DM-93) Scale accession number - Accession number of the scale in a suitable controlled vocabulary (Crop Ontology).", diff --git a/Specification/BrAPI-Schema/BrAPI-Phenotyping/Observation.json b/Specification/BrAPI-Schema/BrAPI-Phenotyping/Observation.json index 3ac614cc..0eecbeaf 100644 --- a/Specification/BrAPI-Schema/BrAPI-Phenotyping/Observation.json +++ b/Specification/BrAPI-Schema/BrAPI-Phenotyping/Observation.json @@ -12,7 +12,8 @@ "type": [ "null", "string" - ] + ], + "example": "917d3ae0" }, "externalReferences": { "description": "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI.", @@ -41,7 +42,8 @@ }, "observationDbId": { "description": "The ID which uniquely identifies an observation", - "type": "string" + "type": "string", + "example": "ef24b615" }, "observationTimeStamp": { "description": "The date and time when this observation was made", @@ -79,14 +81,16 @@ "type": [ "null", "string" - ] + ], + "example": "a2f7f60b" }, "value": { "description": "The value of the data collected as an observation", "type": [ "null", "string" - ] + ], + "example": "2.3" }, "images": { "title": "images", diff --git a/Specification/BrAPI-Schema/BrAPI-Phenotyping/ObservationUnit.json b/Specification/BrAPI-Schema/BrAPI-Phenotyping/ObservationUnit.json index 2c827525..d3cda181 100644 --- a/Specification/BrAPI-Schema/BrAPI-Phenotyping/ObservationUnit.json +++ b/Specification/BrAPI-Schema/BrAPI-Phenotyping/ObservationUnit.json @@ -40,21 +40,24 @@ }, "observationUnitDbId": { "description": "The ID which uniquely identifies an observation unit\n\nMIAPPE V1.1 (DM-70) Observation unit ID - Identifier used to identify the observation unit in data files containing the values observed or measured on that unit. Must be locally unique. ", - "type": "string" + "type": "string", + "example": "8c67503c" }, "observationUnitName": { "description": "A human readable name for an observation unit", "type": [ "null", "string" - ] + ], + "example": "Plot 1" }, "observationUnitPUI": { "description": "A Permanent Unique Identifier for an observation unit\n\nMIAPPE V1.1 (DM-72) External ID - Identifier for the observation unit in a persistent repository, comprises the name of the repository and the identifier of the observation unit therein. The EBI Biosamples repository can be used. URI are recommended when possible.", "type": [ "null", "string" - ] + ], + "example": "http://pui.per/plot/1a9afc14" }, "observationUnitPosition": { "description": "All positional and layout information related to this Observation Unit \n\nMIAPPE V1.1 (DM-73) Spatial distribution - Type and value of a spatial coordinate (georeference or relative) \nor level of observation (plot 45, subblock 7, block 2) provided as a key-value pair of the form type:value. \nLevels of observation must be consistent with those listed in the Study section.", diff --git a/Specification/BrAPI-Schema/BrAPI-Phenotyping/ObservationVariable.json b/Specification/BrAPI-Schema/BrAPI-Phenotyping/ObservationVariable.json index ccd00194..69387d59 100644 --- a/Specification/BrAPI-Schema/BrAPI-Phenotyping/ObservationVariable.json +++ b/Specification/BrAPI-Schema/BrAPI-Phenotyping/ObservationVariable.json @@ -12,18 +12,21 @@ "properties": { "observationVariableDbId": { "description": "Variable unique identifier\n\nMIAPPE V1.1 (DM-83) Variable ID - Code used to identify the variable in the data file. We recommend using a variable definition from the Crop Ontology where possible. Otherwise, the Crop Ontology naming convention is recommended: __). A variable ID must be unique within a given investigation.", - "type": "string" + "type": "string", + "example": "b9b7edd1" }, "observationVariableName": { "description": "Variable name (usually a short name)\n\nMIAPPE V1.1 (DM-84) Variable name - Name of the variable.", - "type": "string" + "type": "string", + "example": "Variable Name" }, "observationVariablePUI": { "description": "The Permanent Unique Identifier of a Observation Variable, usually in the form of a URI", "type": [ "null", "string" - ] + ], + "example": "http://my-traits.com/trait/CO_123:0009012" }, "studies": { "title": "Studies", diff --git a/Specification/BrAPI-Schema/BrAPI-Phenotyping/Ontology.json b/Specification/BrAPI-Schema/BrAPI-Phenotyping/Ontology.json index 0471380b..10e6af16 100644 --- a/Specification/BrAPI-Schema/BrAPI-Phenotyping/Ontology.json +++ b/Specification/BrAPI-Schema/BrAPI-Phenotyping/Ontology.json @@ -12,21 +12,24 @@ "type": [ "null", "string" - ] + ], + "example": "Bob Robertson, Rob Robertson" }, "copyright": { "description": "Ontology copyright", "type": [ "null", "string" - ] + ], + "example": "Copyright 1987, Bob Robertson" }, "description": { "description": "Human readable description of Ontology", "type": [ "null", "string" - ] + ], + "example": "This is an example ontology that does not exist" }, "documentationURL": { "description": "A URL to the human readable documentation of an object", @@ -34,14 +37,16 @@ "type": [ "null", "string" - ] + ], + "example": "https://wiki.brapi.org/ontology" }, "licence": { "description": "Ontology licence", "type": [ "null", "string" - ] + ], + "example": "MIT Open source licence" }, "ontologyDbId": { "description": "Ontology database unique identifier", @@ -49,14 +54,16 @@ }, "ontologyName": { "description": "Ontology name", - "type": "string" + "type": "string", + "example": "The Official Ontology" }, "version": { "description": "Ontology version (no specific format)", "type": [ "null", "string" - ] + ], + "example": "V1.3.2" } }, "required": [ diff --git a/Specification/BrAPI-Schema/BrAPI-Phenotyping/Scale.json b/Specification/BrAPI-Schema/BrAPI-Phenotyping/Scale.json index 9cc0342c..ce5a8691 100644 --- a/Specification/BrAPI-Schema/BrAPI-Phenotyping/Scale.json +++ b/Specification/BrAPI-Schema/BrAPI-Phenotyping/Scale.json @@ -29,7 +29,8 @@ "type": [ "null", "integer" - ] + ], + "example": 2 }, "externalReferences": { "description": "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI.", @@ -55,21 +56,24 @@ }, "scaleName": { "description": "Name of the scale\n
MIAPPE V1.1 (DM-92) Scale Name of the scale associated with the variable", - "type": "string" + "type": "string", + "example": "Meters" }, "scalePUI": { "description": "The Permanent Unique Identifier of a Scale, usually in the form of a URI", "type": [ "null", "string" - ] + ], + "example": "http://my-traits.com/trait/CO_123:0000112" }, "units": { "description": "This field can be used to describe the units used for this scale. This should be the abbreviated \nform of the units, intended to be displayed with every value using this scale. Usually this only \napplies when `dataType` is Numeric, but could also be included for other dataTypes when applicable.", "type": [ "null", "string" - ] + ], + "example": "m" }, "validValues": { "relationshipType": "one-to-one", @@ -115,14 +119,16 @@ "type": [ "null", "string" - ] + ], + "example": "9999" }, "minimumValue": { "description": "Minimum value for numerical, date, and time scales. Typically used for data capture control and QC.", "type": [ "null", "string" - ] + ], + "example": "2" }, "scale": { "description": "associated scale", diff --git a/Specification/BrAPI-Schema/BrAPI-Phenotyping/Trait.json b/Specification/BrAPI-Schema/BrAPI-Phenotyping/Trait.json index 10d25d49..7e5083e0 100644 --- a/Specification/BrAPI-Schema/BrAPI-Phenotyping/Trait.json +++ b/Specification/BrAPI-Schema/BrAPI-Phenotyping/Trait.json @@ -15,35 +15,40 @@ "type": [ "null", "array" - ] + ], + "example": ["H", "PH", "H1"] }, "attribute": { "description": "A trait can be decomposed as \"Trait\" = \"Entity\" + \"Attribute\", the attribute is the observed feature (or characteristic) of the entity e.g., for \"grain colour\", attribute = \"colour\"", "type": [ "null", "string" - ] + ], + "example": "height" }, "attributePUI": { "description": "The Permanent Unique Identifier of a Trait Attribute, usually in the form of a URI\n
A trait can be decomposed as \"Trait\" = \"Entity\" + \"Attribute\", the attribute is the observed feature (or characteristic) of the entity e.g., for \"grain colour\", attribute = \"colour\"", "type": [ "null", "string" - ] + ], + "example": "http://my-traits.com/trait/PO:00012345" }, "entity": { "description": "A trait can be decomposed as \"Trait\" = \"Entity\" + \"Attribute\", the entity is the part of the plant that the trait refers to e.g., for \"grain colour\", entity = \"grain\"", "type": [ "null", "string" - ] + ], + "example": "Stalk" }, "entityPUI": { "description": "The Permanent Unique Identifier of a Trait Entity, usually in the form of a URI\n
A Trait can be decomposed as \"Trait\" = \"Entity\" + \"Attribute\", the Entity is the part of the plant that the trait refers to e.g., for \"grain colour\", entity = \"grain\" ", "type": [ "null", "string" - ] + ], + "example": "http://my-traits.com/trait/PATO:00098765" }, "externalReferences": { "description": "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI.", @@ -63,7 +68,8 @@ "type": [ "null", "string" - ] + ], + "example": "PH" }, "ontologyReference": { "description": "MIAPPE V1.1\n\n(DM-85) Variable accession number - Accession number of the variable in the Crop Ontology\n\n(DM-87) Trait accession number - Accession number of the trait in a suitable controlled vocabulary (Crop Ontology, Trait Ontology).\n\n(DM-89) Method accession number - Accession number of the method in a suitable controlled vocabulary (Crop Ontology, Trait Ontology).\n\n(DM-93) Scale accession number - Accession number of the scale in a suitable controlled vocabulary (Crop Ontology).", @@ -75,7 +81,8 @@ "type": [ "null", "string" - ] + ], + "example": "recommended" }, "synonyms": { "description": "Other trait names", @@ -85,14 +92,16 @@ "type": [ "null", "array" - ] + ], + "example": ["Height", "Plant Height", "Stalk Height", "Canopy Height"] }, "traitClass": { "description": "A classification to describe the type of trait and the context it should be considered in.\n
examples- \"morphological\", \"phenological\", \"agronomical\", \"physiological\", \"abiotic stress\", \"biotic stress\", \"biochemical\", \"quality traits\", \"fertility\", etc.", "type": [ "null", "string" - ] + ], + "example": "phenological" }, "traitDbId": { "description": "The ID which uniquely identifies a trait", @@ -106,18 +115,21 @@ "type": [ "null", "string" - ] + ], + "example": "The height of the plant" }, "traitName": { "description": "The human readable name of a trait\n
MIAPPE V1.1 (DM-86) Trait - Name of the (plant or environmental) trait under observation", - "type": "string" + "type": "string", + "example": "Height" }, "traitPUI": { "description": "The Permanent Unique Identifier of a Trait, usually in the form of a URI", "type": [ "null", "string" - ] + ], + "example": "http://my-traits.com/trait/CO_123:0000012" } }, "required": [