Added missing descriptions and some minor changes in Schema

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

@@ -2,11 +2,18 @@
     "$defs": {
         "AdditionalInfo": {
             "additionalProperties": {
-                "type": "string"
+                "description": "A free space containing any additional information related to a particular object.",
+                "type": [
+                    "null",
+                    "string"
+                ]
             },
             "description": "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification.",
             "title": "AdditionalInfo",
-            "type": "object"
+            "type": [
+                "null",
+                "object"
+            ]
         }
     },
     "$id": "https://brapi.org/Specification/BrAPI-Schema/Components/Common/AdditionalInfo.json",

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

@@ -1,6 +1,7 @@
 {
     "$defs": {
         "DataLink": {
+            "description": "A link to a data file associated with a study. Extra data could include notes, images, and reference data. Based on the MIAPPE V1.1 (DM-38) Data file description.",
             "properties": {
                 "dataFormat": {
                     "description": "The structure of the data within a file. For example - VCF, table, image archive, multispectral image archives in EDAM ontology (used in Galaxy)\n\nMIAPPE V1.1 (DM-38) Data file description - Description of the format of the data file. May be a standard file format name, or a description of organization of the data in a tabular file.",

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

@@ -103,7 +103,10 @@
             "type": "object",
             "description": "A List represents a collection of other BrAPI data objects. Typically these are custom lists generated by a user to keep track of interesting data. For example, a user might build a List of Germplasm that they have manually marked for further study.",
             "brapi-metadata": {
-                "primaryModel": true
+                "primaryModel": true,
+                "subQuery": [
+                    "data"
+                ]
             }
         }
     },

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

@@ -68,10 +68,8 @@
                 "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).",
                     "relationshipType": "one-to-many",
-                    "referencedAttribute": "study",
                     "items": {
-                        "$ref": "../BrAPI-Core/Study.json#/$defs/EnvironmentParameters",
-                        "description": "EnvironmentParameters"
+                        "$ref": "../BrAPI-Core/Study.json#/$defs/EnvironmentParameter"
                     },
                     "title": "EnvironmentParameters",
                     "type": [
@@ -322,7 +320,8 @@
                 "primaryModel": true
             }
         },
-        "EnvironmentParameters": {
+        "EnvironmentParameter": {
+            "description": "An environmental parameter that was 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.",
             "properties": {
                 "description": {
                     "description": "Human-readable value of the environment parameter (defined above) constant within the experiment",
@@ -457,13 +456,15 @@
                     "type": "string"
                 },
                 "timestamp": {
+                    "description": "The timestamp of the update.",
                     "format": "date-time",
                     "type": [
                         "null",
                         "string"
                     ]
                 },
                 "version": {
+                    "description": "The version of the update.",
                     "type": [
                         "null",
                         "string"

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

@@ -238,12 +238,14 @@
         "Publication": {
             "properties": {
                 "publicationPUI": {
+                    "description": "The permanent unique identifier of the publication.",
                     "type": [
                         "null",
                         "string"
                     ]
                 },
                 "publicationReference": {
+                    "description": "The publication reference.",
                     "type": [
                         "null",
                         "string"

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

@@ -67,6 +67,7 @@
             }
         },
         "GenotypeMetadata": {
+            "description": "An additional layer of metadata associated with a genotype",
             "properties": {
                 "dataType": {
                     "description": "The type of field represented in this Genotype Field. This is intended to help parse the data out of JSON.",

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

@@ -65,12 +65,12 @@
                 },
                 "plannedCross": {
                     "$ref": "PlannedCross.json#/$defs/PlannedCross",
-                    "description": "the unique identifier for a planned cross",
+                    "description": "The Cross that was used in the planning of this one.",
                     "referencedAttribute": "crosses",
                     "relationshipType": "many-to-one"
                 },
                 "pollinationEvents": {
-                    "description": "The list of pollination events that occurred for this cross",
+                    "description": "The list of pollination events that occurred for this cross.",
                     "relationshipType": "one-to-many",
                     "referencedAttribute": "cross",
                     "items": {
@@ -132,7 +132,7 @@
                 }
             },
             "title": "CrossAttribute",
-            "description": "A custom attributes associated with a cross",
+            "description": "A custom attribute associated with a cross. For example, if the crossing event occurred on a humid day, a user might record 'crossAttributeName':'Relative Humidity', 'crossAttributeValue':'80%'",
             "type": "object",
             "brapi-metadata": {
                 "primaryModel": false
@@ -163,14 +163,14 @@
                     ]
                 },
                 "cross": {
-                    "description": "Pollination events associated with a cross",
+                    "description": "The Cross associated with this Pollination Event",
                     "$ref": "../BrAPI-Germplasm/Cross.json#/$defs/Cross",
                     "relationshipType": "many-to-one",
                     "referencedAttribute": "pollinationEvents"
                 }
             },
             "title": "PollinationEvent",
-            "description": "A pollination event that occurred for this cross",
+            "description": "A Pollination Event that was used or attempted for a Cross.",
             "type": "object",
             "brapi-metadata": {
                 "primaryModel": false

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

@@ -133,7 +133,7 @@
                     ]
                 },
                 "germplasmDbId": {
-                    "description": "The ID which uniquely identifies a germplasm within the given database server \n<br>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.",
+                    "description": "The ID which uniquely identifies a germplasm within the given database server \n<br>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"
                 },
                 "germplasmName": {
@@ -155,7 +155,7 @@
                     ]
                 },
                 "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, seed 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.",
+                    "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"
                 },
                 "germplasmPreprocessing": {
@@ -245,7 +245,6 @@
                 "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.",
                     "relationshipType": "one-to-many",
-                    "referencedAttribute": "germplasm",
                     "items": {
                         "$ref": "../BrAPI-Germplasm/Germplasm.json#/$defs/Synonym",
                         "description": "Synonyms"
@@ -264,7 +263,6 @@
                         "$ref": "../BrAPI-Germplasm/Germplasm.json#/$defs/TaxonId",
                         "description": "TaxonIds"
                     },
-                    "title": "TaxonIds",
                     "type": [
                         "null",
                         "array"
@@ -408,7 +406,7 @@
                     ]
                 },
                 "germplasm": {
-                    "description": "donoers associated with a germplasm",
+                    "description": "donors associated with a germplasm",
                     "$ref": "../BrAPI-Germplasm/Germplasm.json#/$defs/Germplasm",
                     "relationshipType": "many-to-one",
                     "referencedAttribute": "donors"
@@ -502,6 +500,7 @@
             }
         },
         "Synonym": {
+            "description": "Alternative way to refer to a Germplasm, Cultivar of Variety",
             "properties": {
                 "synonym": {
                     "description": "Alternative name or ID used to reference this germplasm",
@@ -532,6 +531,7 @@
             }
         },
         "TaxonId": {
+            "description": "The Taxon of the Germplasm",
             "properties": {
                 "taxonId": {
                     "description": "The identifier (name, ID, URI) of a particular taxonomy within the source provider",

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

@@ -192,7 +192,7 @@
                 }
             },
             "title": "EventParameter",
-            "description": "An object describing additional event parameters. Each of the following accepts a human-readable value or URI",
+            "description": "Additional metadata to describe an event, based on the ICASA standard model. For example, 'Tillage Implement' (tiimp), 'Tillage Depth' (tidep), and 'Tillage Mix Effectiveness' (timix) might all be recorded parameters for a Tillage event.",
             "type": "object",
             "brapi-metadata": {
                 "primaryModel": false

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

@@ -4,8 +4,7 @@
             "properties": {
                 "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.",
-                    "$ref": "../BrAPI-Common/AdditionalInfo.json#/$defs/AdditionalInfo",
-					"relationshipType": "one-to-one"
+                    "$ref": "../BrAPI-Common/AdditionalInfo.json#/$defs/AdditionalInfo"
                 },
                 "copyright": {
                     "description": "The copyright information of this image. Example 'Copyright 2018 Bob Robertson'",

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

@@ -73,6 +73,7 @@
                 }
             },
             "required": [
+                "methodDbId",
                 "methodName"
             ],
             "title": "Method",

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

@@ -64,6 +64,7 @@
                     "relationshipType": "many-to-one"
                 },
                 "season": {
+                    "description": "The season for this Observation",
                     "$ref": "../BrAPI-Core/Season.json#/$defs/Season",
                     "relationshipType": "many-to-one"
                 },