added descriptions to entities

Specification/BrAPI-Schema/BrAPI-Common/OntologyTerm.json

@@ -30,6 +30,7 @@
                 }
             },
             "title": "OntologyTerm",
+            "description": "A pointer to an ontology used by a genomic reference",
             "type": "object",
             "brapi-metadata": {
                 "primaryModel": false

Specification/BrAPI-Schema/BrAPI-Common/Variable.json

@@ -132,6 +132,7 @@
                 "scale"
             ],
             "title": "Variable",
+            "description": "A unique combination of Trait, Method, and Scale to define a clear context for an Observation.",
             "type": "object",
             "brapi-metadata": {
                 "interface": true

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

@@ -47,6 +47,7 @@
             ],
             "type": "object",
             "title": "Contact",
+            "description": "A persons contact information",
             "brapi-metadata": {
                 "primaryModel": false
             }

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

@@ -61,6 +61,7 @@
                 }
             },
             "title": "DataLink",
+            "description": "A link to extra data files associated with this study. Extra data could include notes, images, and reference data.",
             "type": "object",
             "brapi-metadata": {
                 "primaryModel": false

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

@@ -200,6 +200,7 @@
                 "locationName"
             ],
             "title": "Location",
+            "description": "A geographic Location on earth. This is usually used to describe the general area where an experiment took place. For example, a natural site, an experimental field, a greenhouse, a phenotyping facility, etc.",
             "type": "object",
             "brapi-metadata": {
                 "primaryModel": true

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

@@ -113,6 +113,7 @@
                 "personDbId"
             ],
             "title": "Person",
+            "description": "A generic object used to maintain the metadata needed to describe a human. The Person might be a software user, a field technician, or a primary contact for a Program.",
             "type": "object",
             "brapi-metadata": {
                 "primaryModel": true

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

@@ -172,6 +172,7 @@
                 "programName"
             ],
             "title": "Program",
+            "description": "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. A Program can contain multiple Trials. A Trial can contain multiple Studies.",
             "type": "object",
             "brapi-metadata": {
                 "primaryModel": true

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

@@ -25,6 +25,7 @@
                 "seasonDbId"
             ],
             "title": "Season",
+            "description": "A Season defines a period in time. A Season is made of two parts; (1) the primary year and (2) a term which defines a segment of the year. This term could be a traditional season, like \"Spring\" or \"Summer\", or this term could be a month, like \"May\" or \"June\", or this could be an arbitrary season name which is meaningful to the breeding Program like \"PlantingTime_3\" or \"Season E\".",
             "type": "object",
             "brapi-metadata": {
                 "primaryModel": true

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

@@ -316,6 +316,7 @@
                 "studyDbId"
             ],
             "title": "Study",
+            "description": "A Study represents an experiment that has taken place at a single location. The Study contains metadata about the parameters and design of the experiment. It can also be used to group results and data sets generated from the experiment. A Trial can represent a collection of one or more Studies.",
             "type": "object",
             "brapi-metadata": {
                 "primaryModel": true
@@ -383,6 +384,7 @@
                 "description"
             ],
             "title": "EnvironmentParameters",
+            "description": "Environmental parameters that were kept constant throughout the study and did not change between observation units. \n\nMIAPPE V1.1 (DM-57) Environment - Environmental parameters that were kept constant throughout the study and did not change between observation units or assays. Environment characteristics that vary over time, i.e. environmental variables, should be recorded as Observed Variables (see below).",
             "type": "object",
             "brapi-metadata": {
                 "primaryModel": false
@@ -412,6 +414,7 @@
                 }
             },
             "title": "ExperimentalDesign",
+            "description": "The experimental and statistical design full description plus a category PUI taken from crop research ontology or agronomy ontology",
             "type": "object",
             "brapi-metadata": {
                 "primaryModel": false
@@ -441,6 +444,7 @@
                 }
             },
             "title": "GrowthFacility",
+            "description": "Short description of the facility in which the study was carried out.",
             "type": "object",
             "brapi-metadata": {
                 "primaryModel": false
@@ -476,6 +480,7 @@
                 "lastUpdateDbId"
             ],
             "title": "LastUpdate",
+            "description": "The date and time when this study was last modified",
             "type": "object",
             "brapi-metadata": {
                 "primaryModel": false

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

@@ -185,6 +185,7 @@
                 "trialDbId"
             ],
             "title": "Trial",
+            "description": "A Trial represents a collection of Study objects, and the metadata associated with that collection. A Trial could represent a multi-location experiment, and could contain information related to publications and data licensing.",
             "type": "object",
             "brapi-metadata": {
                 "primaryModel": true
@@ -228,6 +229,7 @@
                 }
             },
             "title": "DatasetAuthorships",
+            "description": "License and citation information for the data in this trial",
             "type": "object",
             "brapi-metadata": {
                 "primaryModel": false
@@ -255,6 +257,7 @@
                 }
             },
             "title": "Publication",
+            "description": "MIAPPE V1.1 (DM-9) Associated publication - An identifier for a literature publication where the investigation is described. Use of DOIs is recommended.",
             "type": "object",
             "brapi-metadata": {
                 "primaryModel": false

Specification/BrAPI-Schema/BrAPI-Genotyping/AlleleMatrix.json

@@ -91,6 +91,7 @@
                 "variantSets"
             ],
             "title": "AlleleMatrix",
+            "description": "The AlleleMatrix 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.",
             "type": "object",
             "brapi-metadata": {
                 "primaryModel": true
@@ -149,6 +150,7 @@
                 }
             },
             "title": "DataMatrix",
+            "description": "A two dimensional array that holds allele data or associated metadata. Each matrix should be the same size and orientation, aligned with the \"callSetDbIds\" as columns and the \"variantDbIds\" as rows.",
             "type": "object",
             "brapi-metadata": {
                 "primaryModel": false
@@ -204,6 +206,7 @@
                 }
             },
             "title": "Pagination",
+            "description": "Pagination info for the matrix",
             "type": "object",
             "brapi-metadata": {
                 "primaryModel": false

Specification/BrAPI-Schema/BrAPI-Genotyping/Call.json

@@ -60,6 +60,7 @@
                 "variantSet"
             ],
             "title": "Call",
+            "description": "A `Call` represents the determination of genotype with respect to a particular `Variant`. \n\nIt may include associated information such as quality and phasing. For example, a call might assign a probability of 0.32 to the occurrence of a SNP named RS_1234 in a call set with the name NA_12345.",
             "type": "object",
             "brapi-metadata": {
                 "primaryModel": true
@@ -110,6 +111,7 @@
                 }
             },
             "title": "GenotypeMetadata",
+            "description": "Genotype Metadata are additional layers of metadata associated with each genotype.",
             "type": "object",
             "brapi-metadata": {
                 "primaryModel": false

Specification/BrAPI-Schema/BrAPI-Genotyping/CallSet.json

@@ -101,6 +101,7 @@
                 "callSetDbId"
             ],
             "title": "CallSet",
+            "description": "A CallSet is a collection of Calls that were generated by the same analysis of the same Sample",
             "type": "object",
             "brapi-metadata": {
                 "primaryModel": true

Specification/BrAPI-Schema/BrAPI-Genotyping/GenomeMap.json

@@ -108,6 +108,7 @@
                 "type"
             ],
             "title": "GenomeMap",
+            "description": "The GenomeMap represents the metadata associated with a reference map of a particular species genome. A GenomeMap can either represent a physical map or genetic map.",
             "type": "object",
             "brapi-metadata": {
                 "primaryModel": true

Specification/BrAPI-Schema/BrAPI-Genotyping/MarkerPosition.json

@@ -35,6 +35,7 @@
                 }
             },
             "title": "MarkerPosition",
+            "description": "A MarkerPosition describes a particular genetic marker at a specific position on a GenomeMap. A collection of MarkerPositions make up the data to represent a full GenomeMap.",
             "type": "object",
             "brapi-metadata": {
                 "primaryModel": true

Specification/BrAPI-Schema/BrAPI-Genotyping/Plate.json

@@ -98,6 +98,7 @@
                 "plateName"
             ],
             "title": "Plate",
+            "description": "A Plate represents the metadata for a collection of Samples. The physical Plate being represented might be a plastic tray full of Samples, or a group of Samples stored in individual containers ie bags, test tubes, etc. Whatever the container is, the Samples in a Plate should be related by the same physical space, though they may or may not be related as part of the same experiment or analysis.",
             "type": "object",
             "brapi-metadata": {
                 "primaryModel": true

Specification/BrAPI-Schema/BrAPI-Genotyping/Reference.json

@@ -126,6 +126,7 @@
                 "referenceName"
             ],
             "title": "Reference",
+            "description": "A `Reference` is a canonical assembled contig, intended to act as a reference coordinate space for other genomic annotations. A single `Reference` might represent the human chromosome 1, for instance. `References` are designed to be immutable.",
             "type": "object",
             "brapi-metadata": {
                 "primaryModel": true

Specification/BrAPI-Schema/BrAPI-Genotyping/ReferenceSet.json

@@ -141,6 +141,7 @@
                 "referenceSetName"
             ],
             "title": "ReferenceSet",
+            "description": "A `ReferenceSet` is a set of `Reference` s which typically comprise a reference assembly, such as `GRCH_38`. A `ReferenceSet` defines a common coordinate space for comparing reference-aligned experimental data.",
             "type": "object",
             "brapi-metadata": {
                 "primaryModel": true

Specification/BrAPI-Schema/BrAPI-Genotyping/Sample.json

@@ -166,6 +166,7 @@
                 "sampleName"
             ],
             "title": "Sample",
+            "description": "The identifiers and metadata associated with a physical piece of biological material collected from the field for external analysis. A Sample can take many forms (leaf clipping, seed, DNA, etc) and might be used for a variety of analysis procedures (spectra, genotyping, etc).",
             "type": "object",
             "brapi-metadata": {
                 "primaryModel": true

Specification/BrAPI-Schema/BrAPI-Genotyping/Variant.json

@@ -204,6 +204,7 @@
                 "variantDbId"
             ],
             "title": "Variant",
+            "description": "A `Variant` represents a change in DNA sequence relative to some reference. For example, a variant could represent a classic marker, a SNP, or an insertion. This is equivalent to a row in VCF.",
             "type": "object",
             "brapi-metadata": {
                 "primaryModel": true

Specification/BrAPI-Schema/BrAPI-Genotyping/VariantSet.json

@@ -156,6 +156,7 @@
                 "variantSetDbId"
             ],
             "title": "VariantSet",
+            "description": "A VariantSet is a collection of variants and variant calls intended to be analyzed together.",
             "type": "object",
             "brapi-metadata": {
                 "primaryModel": true
@@ -228,6 +229,7 @@
                 "analysisDbId"
             ],
             "title": "Analysis",
+            "description": "An analysis contains an interpretation of one or several experiments. (e.g. SNVs, copy number variations, methylation status) together with information about the methodology used.",
             "type": "object",
             "brapi-metadata": {
                 "primaryModel": false
@@ -309,6 +311,7 @@
                 }
             },
             "title": "AvailableFormat",
+            "description": "Each 'availableFormat' object is a pairing of dataFormat and fileFormat. These must be communicated in pairs because they are not independent parameters and sometimes one influences the other.",
             "type": "object",
             "brapi-metadata": {
                 "primaryModel": false
@@ -352,6 +355,7 @@
                 }
             },
             "title": "MetadataField",
+            "description": "Indicates which types of genotyping data and metadata are available in the VariantSet. \n<br> When possible, these field names and abbreviations should follow the VCF standard ",
             "type": "object",
             "brapi-metadata": {
                 "primaryModel": false

Specification/BrAPI-Schema/BrAPI-Germplasm/BreedingMethod.json

@@ -63,6 +63,7 @@
                 "description"
             ],
             "title": "Breeding Method",
+            "description": "The techniques and protocol used to produce a Cross or Germplasm",
             "type": "object",
             "brapi-metadata": {
                 "primaryModel": true

Specification/BrAPI-Schema/BrAPI-Germplasm/Cross.json

@@ -102,6 +102,7 @@
                 "crossDbId"
             ],
             "title": "Cross",
+            "description": "The identifiers and metadata represent that specific organisms have mated to produce offspring with particular traits or genes. The offspring of a Cross might be developed into a Germplasm if the desired traits are present.",
             "type": "object",
             "brapi-metadata": {
                 "primaryModel": true
@@ -131,6 +132,7 @@
                 }
             },
             "title": "CrossAttribute",
+            "description": "A custom attributes associated with a cross",
             "type": "object",
             "brapi-metadata": {
                 "primaryModel": false
@@ -168,6 +170,7 @@
                 }
             },
             "title": "PollinationEvent",
+            "description": "A pollination event that occurred for this cross",
             "type": "object",
             "brapi-metadata": {
                 "primaryModel": false

Specification/BrAPI-Schema/BrAPI-Germplasm/CrossParent.json

@@ -26,6 +26,7 @@
                 }
             },
             "title": "CrossParent",
+            "description": "The identifying information gor the parent material of a cross.",
             "type": "object",
             "brapi-metadata": {
                 "primaryModel": false

Specification/BrAPI-Schema/BrAPI-Germplasm/CrossingProject.json

@@ -106,6 +106,7 @@
                 "crossingProjectName"
             ],
             "title": "CrossingProject",
+            "description": "A project structure where a list of PlannedCrosses is generated, the crossing events occur in the field, and the resulting actual Crosses can documented.",
             "type": "object",
             "brapi-metadata": {
                 "primaryModel": true

Specification/BrAPI-Schema/BrAPI-Germplasm/Germplasm.json

@@ -385,6 +385,7 @@
                 "commonCropName"
             ],
             "title": "Germplasm",
+            "description": "The conceptual identifiers and metadata describing a genetically unique organism that is noteworthy in some way. Depending on context, a Germplasm might be synonymous with Accession, Line, or Genotype. Note that Germplasm is conceptual data, not necessarily associated to a real physical object, so Seed/Inventory Lots and Observation Units become physical instantiations of a particular Germplasm. Note a Germplasm is unique and noteworthy, so a Cross may or may not create a new Germplasm, since not every Cross is unique or noteworthy.",
             "type": "object",
             "brapi-metadata": {
                 "primaryModel": true
@@ -414,6 +415,7 @@
                 }
             },
             "title": "Donor",
+            "description": "Identifier assigned to an accession by the material donor.",
             "type": "object",
             "brapi-metadata": {
                 "primaryModel": false
@@ -450,6 +452,7 @@
                 }
             },
             "title": "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.",
             "type": "object",
             "brapi-metadata": {
                 "primaryModel": false
@@ -492,6 +495,7 @@
                 }
             },
             "title": "StorageType",
+            "description": "The type of storage this germplasm is kept in at a genebank.",
             "type": "object",
             "brapi-metadata": {
                 "primaryModel": false
@@ -521,6 +525,7 @@
                 }
             },
             "title": "Synonym",
+            "description": "Alternative names or IDs used to reference this germplasm",
             "type": "object",
             "brapi-metadata": {
                 "primaryModel": false
@@ -548,6 +553,7 @@
                 "taxonId"
             ],
             "title": "TaxonId",
+            "description": "The list of IDs for this SPECIES from different sources. If present, NCBI Taxon should be always listed as \"ncbiTaxon\" preferably with a purl. The rank of this ID should be species. \n\nMIAPPE V1.1 (DM-42) Organism - An identifier for the organism at the species level. Use of the NCBI taxon ID is recommended.",
             "type": "object",
             "brapi-metadata": {
                 "primaryModel": false

Specification/BrAPI-Schema/BrAPI-Germplasm/GermplasmAttribute.json

@@ -26,6 +26,7 @@
                 }
             ],
             "title": "GermplasmAttribute",
+            "description": "The Trait-Method-Scale definition for a variable, specifically variables related to Germplasm. Similar to an ObservationVariable, but related to a Germplasm instead of an ObservationUnit",
             "brapi-metadata": {
                 "primaryModel": true
             }

Specification/BrAPI-Schema/BrAPI-Germplasm/GermplasmAttributeValue.json

@@ -56,6 +56,7 @@
                 "attribute"
             ],
             "title": "GermplasmAttributeValue",
+            "description": "The value recorded for a particular Trait/Attribute and a particular Germplasm. Similar to an Observation value, but more concrete, applying to the whole Germplasm instead of a single ObservationUnit.",
             "type": "object",
             "brapi-metadata": {
                 "primaryModel": true

Specification/BrAPI-Schema/BrAPI-Germplasm/PedigreeNode.json

@@ -118,6 +118,7 @@
                 "germplasm"
             ],
             "title": "PedigreeNode",
+            "description": "A representation of a particular Germplasm within a pedigree tree, and all the links to its parents, siblings, and children. From a list of PedigreeNode objects, a client application should have all the information it needs to draw a pedigree tree visualization, or calculate genetic distances.",
             "type": "object",
             "brapi-metadata": {
                 "primaryModel": true
@@ -147,6 +148,7 @@
                 "parentType"
             ],
             "title": "GermplasmParent",
+            "description": "A germplasm reference that is a direct parent of this germplasm. These represent edges in the tree, connecting to other nodes.",
             "type": "object",
             "brapi-metadata": {
                 "primaryModel": false
@@ -176,6 +178,7 @@
                 "parentType"
             ],
             "title": "GermplasmChild",
+            "description": "A germplasm reference that is a direct child of this germplasm. These represent edges in the tree, connecting to other nodes.",
             "type": "object",
             "brapi-metadata": {
                 "primaryModel": false