From 0d7705498656359a5375c5a745d5cb38dcfd8e7b Mon Sep 17 00:00:00 2001 From: Peter Selby Date: Wed, 5 Dec 2018 14:49:24 -0500 Subject: [PATCH] update READMEs --- Specification/GermplasmAttributes/README.md | 16 +- Specification/Images/README.md | 4 +- Specification/Lists/README.md | 10 +- Specification/MarkerProfiles/README.md | 8 +- Specification/ObservationVariables/README.md | 196 +++++---- Specification/People/README.md | 2 +- Specification/Phenotypes/README.md | 4 +- Specification/Samples/README.md | 4 +- Specification/Studies/README.md | 404 ++----------------- 9 files changed, 195 insertions(+), 453 deletions(-) diff --git a/Specification/GermplasmAttributes/README.md b/Specification/GermplasmAttributes/README.md index 67515a24..70d1c0ae 100644 --- a/Specification/GermplasmAttributes/README.md +++ b/Specification/GermplasmAttributes/README.md @@ -130,7 +130,7 @@ List available attributes. "methodDbId": "m1", "methodName": "Tape Measure", "name": "Tape Measure", - "ontologyRefernce": { + "ontologyReference": { "documentationLinks": [ { "URL": "https://ontology.org/m1", @@ -147,7 +147,7 @@ List available attributes. "name": "Rht-B1b", "ontologyDbId": "MO_123", "ontologyName": "Ontology.org", - "ontologyRefernce": { + "ontologyReference": { "documentationLinks": [ { "URL": "https://ontology.org", @@ -163,7 +163,7 @@ List available attributes. "dataType": "Numerical", "decimalPlaces": 1, "name": "Centimeter", - "ontologyRefernce": { + "ontologyReference": { "documentationLinks": [ { "URL": "https://ontology.org/s1", @@ -196,7 +196,7 @@ List available attributes. "entity": "entity", "mainAbbreviation": "H", "name": "Plant Height", - "ontologyRefernce": { + "ontologyReference": { "documentationLinks": [ { "URL": "https://ontology.org/t1", @@ -239,7 +239,7 @@ List available attributes. "methodDbId": "m3", "methodName": "Standard Color Palette", "name": "Standard Color Palette", - "ontologyRefernce": { + "ontologyReference": { "documentationLinks": [ { "URL": "https://ontology.org/m3", @@ -256,7 +256,7 @@ List available attributes. "name": "Weevil Resistance", "ontologyDbId": "MO_123", "ontologyName": "Ontology.org", - "ontologyRefernce": { + "ontologyReference": { "documentationLinks": [ { "URL": "https://ontology.org", @@ -272,7 +272,7 @@ List available attributes. "dataType": "Nominal", "decimalPlaces": 0, "name": "Color", - "ontologyRefernce": { + "ontologyReference": { "documentationLinks": [ { "URL": "https://ontology.org/s3", @@ -311,7 +311,7 @@ List available attributes. "entity": "entity", "mainAbbreviation": "LC", "name": "Leaf Color", - "ontologyRefernce": { + "ontologyReference": { "documentationLinks": [ { "URL": "https://ontology.org/t3", diff --git a/Specification/Images/README.md b/Specification/Images/README.md index 1be29f7f..edbbb451 100644 --- a/Specification/Images/README.md +++ b/Specification/Images/README.md @@ -224,7 +224,7 @@ Implementation Notes "brapi", "logo" ], - "imageDbId": "60ff3c3b-986b-4c57-8650-5968f66ced28", + "imageDbId": "ce15937e-093e-4624-8950-00dab3172e4c", "imageFileName": "brapi-logo.svg", "imageFileSize": 3676, "imageHeight": 56, @@ -780,7 +780,7 @@ Implementation Notes "brapi", "logo" ], - "imageDbId": "60ff3c3b-986b-4c57-8650-5968f66ced28", + "imageDbId": "ce15937e-093e-4624-8950-00dab3172e4c", "imageFileName": "brapi-logo.svg", "imageFileSize": 3676, "imageHeight": 56, diff --git a/Specification/Lists/README.md b/Specification/Lists/README.md index 050db2e3..5a9d6a37 100644 --- a/Specification/Lists/README.md +++ b/Specification/Lists/README.md @@ -141,10 +141,10 @@ Create a new list "data": [ "string" ], - "dateCreated": "2018-12-04T17:21:06-05:00", - "dateModified": "2018-12-04T17:21:06-05:00", + "dateCreated": "2018-12-05T14:36:04-05:00", + "dateModified": "2018-12-05T14:36:04-05:00", "description": "string", - "listDbId": "cb685990-675c-4700-a78d-eabe908185db", + "listDbId": "d93d6bb6-dfc3-4d15-8d2e-654c618ce12e", "listName": "string", "listOwnerName": "string", "listOwnerPersonDbId": "string", @@ -297,7 +297,7 @@ Update an existing generic list "string" ], "dateCreated": "2011-06-14T22:12:51-04:00", - "dateModified": "2018-12-04T17:21:06-05:00", + "dateModified": "2018-12-05T14:36:04-05:00", "description": "string", "listDbId": "list1", "listName": "string", @@ -375,7 +375,7 @@ Add new data to a specific generic lists "3" ], "dateCreated": "2011-06-14T22:12:51-04:00", - "dateModified": "2018-12-04T17:21:06-05:00", + "dateModified": "2018-12-05T14:36:04-05:00", "description": "string", "listDbId": "list1", "listName": "string", diff --git a/Specification/MarkerProfiles/README.md b/Specification/MarkerProfiles/README.md index 81b7dda0..59cdc2c3 100644 --- a/Specification/MarkerProfiles/README.md +++ b/Specification/MarkerProfiles/README.md @@ -164,9 +164,9 @@ The format of the tsv response can be found on GitHub (https://github.com/plantb "metadata": { "asynchStatus": { "asynchId": "", - "endTime": "2018-12-04", + "endTime": "2018-12-05", "percentComplete": 100, - "startTime": "2018-12-04", + "startTime": "2018-12-05", "status": "FINISHED" }, "datafiles": [], @@ -353,9 +353,9 @@ This method may support asynchronous processing. "metadata": { "asynchStatus": { "asynchId": "", - "endTime": "2018-12-04", + "endTime": "2018-12-05", "percentComplete": 100, - "startTime": "2018-12-04", + "startTime": "2018-12-05", "status": "FINISHED" }, "datafiles": [], diff --git a/Specification/ObservationVariables/README.md b/Specification/ObservationVariables/README.md index 39737c31..ce2f0fba 100644 --- a/Specification/ObservationVariables/README.md +++ b/Specification/ObservationVariables/README.md @@ -52,7 +52,7 @@ An Observation Variable has 3 critical parts: A Trait being observed, a Method f "methodDbId": "m1", "methodName": "Tape Measure", "name": "Tape Measure", - "ontologyRefernce": { + "ontologyReference": { "documentationLinks": [ { "URL": "https://ontology.org/m1", @@ -73,7 +73,7 @@ An Observation Variable has 3 critical parts: A Trait being observed, a Method f "methodDbId": "m2", "methodName": "Dry Electric Scale", "name": "Dry Electric Scale", - "ontologyRefernce": { + "ontologyReference": { "documentationLinks": [ { "URL": "https://ontology.org/m2", @@ -132,9 +132,19 @@ Create a new method object in the database "formula": "formula0", "methodName": "methodName0", "ontologyReference": { - "ontologyID": "ontologyID0", - "ontologyPrefix": "ontologyPrefix0", - "ontologyTerm": "ontologyTerm0" + "documentationLinks": [ + { + "URL": "URL0", + "type": "OBO" + }, + { + "URL": "URL1", + "type": "RDF" + } + ], + "ontologyDbId": "ontologyDbId0", + "ontologyName": "ontologyName0", + "version": "version0" }, "reference": "reference0" } @@ -159,10 +169,10 @@ Create a new method object in the database "class": "string", "description": "string", "formula": "string", - "methodDbId": "ded56cdc-ab8b-4c93-b286-4a1471390b75", + "methodDbId": "8175d7ac-6221-4e1d-8023-91ddb8b30fd8", "methodName": "string", "name": "string", - "ontologyRefernce": { + "ontologyReference": { "documentationLinks": [ { "URL": "string", @@ -235,7 +245,7 @@ An Observation Variable has 3 critical parts: A Trait being observed, a Method f "methodDbId": "m1", "methodName": "Tape Measure", "name": "Tape Measure", - "ontologyRefernce": { + "ontologyReference": { "documentationLinks": [ { "URL": "https://ontology.org/m1", @@ -298,9 +308,19 @@ Update the details of an existing method "formula": "formula0", "methodName": "methodName0", "ontologyReference": { - "ontologyID": "ontologyID0", - "ontologyPrefix": "ontologyPrefix0", - "ontologyTerm": "ontologyTerm0" + "documentationLinks": [ + { + "URL": "URL0", + "type": "OBO" + }, + { + "URL": "URL1", + "type": "RDF" + } + ], + "ontologyDbId": "ontologyDbId0", + "ontologyName": "ontologyName0", + "version": "version0" }, "reference": "reference0" } @@ -328,7 +348,7 @@ Update the details of an existing method "methodDbId": "m1", "methodName": "string", "name": "string", - "ontologyRefernce": { + "ontologyReference": { "documentationLinks": [ { "URL": "string", @@ -477,7 +497,7 @@ An Observation Variable has 3 critical parts: A Trait being observed, a Method f "dataType": "Numerical", "decimalPlaces": 1, "name": "Centimeter", - "ontologyRefernce": { + "ontologyReference": { "documentationLinks": [ { "URL": "https://ontology.org/s1", @@ -502,7 +522,7 @@ An Observation Variable has 3 critical parts: A Trait being observed, a Method f "dataType": "Numerical", "decimalPlaces": 3, "name": "Kilogram", - "ontologyRefernce": { + "ontologyReference": { "documentationLinks": [ { "URL": "https://ontology.org/s2", @@ -566,9 +586,19 @@ Create a new scale object in the database "dataType": "Code", "decimalPlaces": 0, "ontologyReference": { - "ontologyID": "ontologyID0", - "ontologyPrefix": "ontologyPrefix0", - "ontologyTerm": "ontologyTerm0" + "documentationLinks": [ + { + "URL": "URL0", + "type": "OBO" + }, + { + "URL": "URL1", + "type": "RDF" + } + ], + "ontologyDbId": "ontologyDbId0", + "ontologyName": "ontologyName0", + "version": "version0" }, "scaleName": "scaleName0", "validValues": { @@ -602,7 +632,7 @@ Create a new scale object in the database "dataType": "Code", "decimalPlaces": 0, "name": "string", - "ontologyRefernce": { + "ontologyReference": { "documentationLinks": [ { "URL": "string", @@ -614,7 +644,7 @@ Create a new scale object in the database "ontologyName": "Ontology.org", "version": "17" }, - "scaleDbId": "81db1ded-3b7c-4d40-8121-efd412375cd4", + "scaleDbId": "90fdedbc-6412-47ac-877b-81dd466fe6d2", "scaleName": "string", "validValues": { "categories": [ @@ -681,7 +711,7 @@ An Observation Variable has 3 critical parts: A Trait being observed, a Method f "dataType": "Numerical", "decimalPlaces": 1, "name": "Centimeter", - "ontologyRefernce": { + "ontologyReference": { "documentationLinks": [ { "URL": "https://ontology.org/s1", @@ -749,9 +779,19 @@ Update the details of an existing scale "dataType": "Code", "decimalPlaces": 0, "ontologyReference": { - "ontologyID": "ontologyID0", - "ontologyPrefix": "ontologyPrefix0", - "ontologyTerm": "ontologyTerm0" + "documentationLinks": [ + { + "URL": "URL0", + "type": "OBO" + }, + { + "URL": "URL1", + "type": "RDF" + } + ], + "ontologyDbId": "ontologyDbId0", + "ontologyName": "ontologyName0", + "version": "version0" }, "scaleName": "scaleName0", "validValues": { @@ -785,7 +825,7 @@ Update the details of an existing scale "dataType": "Code", "decimalPlaces": 0, "name": "string", - "ontologyRefernce": { + "ontologyReference": { "documentationLinks": [ { "URL": "string", @@ -982,7 +1022,7 @@ See Search Services for additional implementation details. { "contextOfUse": [], "crop": "maize", - "date": "2018-12-04", + "date": "2018-12-05", "defaultValue": "10", "documentationURL": "https://brapi.org", "growthStage": "1", @@ -995,7 +1035,7 @@ See Search Services for additional implementation details. "methodDbId": "m1", "methodName": "Tape Measure", "name": "Tape Measure", - "ontologyRefernce": { + "ontologyReference": { "documentationLinks": [ { "URL": "https://ontology.org/m1", @@ -1014,7 +1054,7 @@ See Search Services for additional implementation details. "observationVariableName": "Plant height", "ontologyDbId": "MO_123", "ontologyName": "Ontology.org", - "ontologyRefernce": { + "ontologyReference": { "documentationLinks": [ { "URL": "https://ontology.org", @@ -1030,7 +1070,7 @@ See Search Services for additional implementation details. "dataType": "Numerical", "decimalPlaces": 1, "name": "Centimeter", - "ontologyRefernce": { + "ontologyReference": { "documentationLinks": [ { "URL": "https://ontology.org/s1", @@ -1063,7 +1103,7 @@ See Search Services for additional implementation details. "entity": "entity", "mainAbbreviation": "H", "name": "Plant Height", - "ontologyRefernce": { + "ontologyReference": { "documentationLinks": [ { "URL": "https://ontology.org/t1", @@ -1086,7 +1126,7 @@ See Search Services for additional implementation details. { "contextOfUse": [], "crop": "maize", - "date": "2018-12-04", + "date": "2018-12-05", "defaultValue": "10", "documentationURL": "https://brapi.org", "growthStage": "1", @@ -1099,7 +1139,7 @@ See Search Services for additional implementation details. "methodDbId": "m3", "methodName": "Standard Color Palette", "name": "Standard Color Palette", - "ontologyRefernce": { + "ontologyReference": { "documentationLinks": [ { "URL": "https://ontology.org/m3", @@ -1118,7 +1158,7 @@ See Search Services for additional implementation details. "observationVariableName": "Carotenoid", "ontologyDbId": "MO_123", "ontologyName": "Ontology.org", - "ontologyRefernce": { + "ontologyReference": { "documentationLinks": [ { "URL": "https://ontology.org", @@ -1134,7 +1174,7 @@ See Search Services for additional implementation details. "dataType": "Nominal", "decimalPlaces": 0, "name": "Color", - "ontologyRefernce": { + "ontologyReference": { "documentationLinks": [ { "URL": "https://ontology.org/s3", @@ -1173,7 +1213,7 @@ See Search Services for additional implementation details. "entity": "entity", "mainAbbreviation": "LC", "name": "Leaf Color", - "ontologyRefernce": { + "ontologyReference": { "documentationLinks": [ { "URL": "https://ontology.org/t3", @@ -1332,9 +1372,19 @@ Create a new trait object in the database "entity": "entity0", "mainAbbreviation": "mainAbbreviation0", "ontologyReference": { - "ontologyID": "ontologyID0", - "ontologyPrefix": "ontologyPrefix0", - "ontologyTerm": "ontologyTerm0" + "documentationLinks": [ + { + "URL": "URL0", + "type": "OBO" + }, + { + "URL": "URL1", + "type": "RDF" + } + ], + "ontologyDbId": "ontologyDbId0", + "ontologyName": "ontologyName0", + "version": "version0" }, "status": "status0", "synonyms": [ @@ -1371,7 +1421,7 @@ Create a new trait object in the database "entity": "string", "mainAbbreviation": "string", "name": "string", - "ontologyRefernce": { + "ontologyReference": { "documentationLinks": [ { "URL": "string", @@ -1387,7 +1437,7 @@ Create a new trait object in the database "synonyms": [ "string" ], - "traitDbId": "166e5017-d160-4435-9cfb-86815e6a41e3", + "traitDbId": "2d078dee-3d06-4deb-b0bb-2919c021a538", "traitName": "string", "xref": "string" } @@ -1509,9 +1559,19 @@ Update an existing trait "entity": "entity0", "mainAbbreviation": "mainAbbreviation0", "ontologyReference": { - "ontologyID": "ontologyID0", - "ontologyPrefix": "ontologyPrefix0", - "ontologyTerm": "ontologyTerm0" + "documentationLinks": [ + { + "URL": "URL0", + "type": "OBO" + }, + { + "URL": "URL1", + "type": "RDF" + } + ], + "ontologyDbId": "ontologyDbId0", + "ontologyName": "ontologyName0", + "version": "version0" }, "status": "status0", "synonyms": [ @@ -1548,7 +1608,7 @@ Update an existing trait "entity": "string", "mainAbbreviation": "string", "name": "string", - "ontologyRefernce": { + "ontologyReference": { "documentationLinks": [ { "URL": "string", @@ -1669,7 +1729,7 @@ See Search Services for additional implementation details. { "contextOfUse": [], "crop": "maize", - "date": "2018-12-04", + "date": "2018-12-05", "defaultValue": "10", "documentationURL": "https://brapi.org", "growthStage": "1", @@ -1682,7 +1742,7 @@ See Search Services for additional implementation details. "methodDbId": "m1", "methodName": "Tape Measure", "name": "Tape Measure", - "ontologyRefernce": { + "ontologyReference": { "documentationLinks": [ { "URL": "https://ontology.org/m1", @@ -1701,7 +1761,7 @@ See Search Services for additional implementation details. "observationVariableName": "Plant height", "ontologyDbId": "MO_123", "ontologyName": "Ontology.org", - "ontologyRefernce": { + "ontologyReference": { "documentationLinks": [ { "URL": "https://ontology.org", @@ -1717,7 +1777,7 @@ See Search Services for additional implementation details. "dataType": "Numerical", "decimalPlaces": 1, "name": "Centimeter", - "ontologyRefernce": { + "ontologyReference": { "documentationLinks": [ { "URL": "https://ontology.org/s1", @@ -1750,7 +1810,7 @@ See Search Services for additional implementation details. "entity": "entity", "mainAbbreviation": "H", "name": "Plant Height", - "ontologyRefernce": { + "ontologyReference": { "documentationLinks": [ { "URL": "https://ontology.org/t1", @@ -1773,7 +1833,7 @@ See Search Services for additional implementation details. { "contextOfUse": [], "crop": "maize", - "date": "2018-12-04", + "date": "2018-12-05", "defaultValue": "10", "documentationURL": "https://brapi.org", "growthStage": "1", @@ -1786,7 +1846,7 @@ See Search Services for additional implementation details. "methodDbId": "m3", "methodName": "Standard Color Palette", "name": "Standard Color Palette", - "ontologyRefernce": { + "ontologyReference": { "documentationLinks": [ { "URL": "https://ontology.org/m3", @@ -1805,7 +1865,7 @@ See Search Services for additional implementation details. "observationVariableName": "Carotenoid", "ontologyDbId": "MO_123", "ontologyName": "Ontology.org", - "ontologyRefernce": { + "ontologyReference": { "documentationLinks": [ { "URL": "https://ontology.org", @@ -1821,7 +1881,7 @@ See Search Services for additional implementation details. "dataType": "Nominal", "decimalPlaces": 0, "name": "Color", - "ontologyRefernce": { + "ontologyReference": { "documentationLinks": [ { "URL": "https://ontology.org/s3", @@ -1860,7 +1920,7 @@ See Search Services for additional implementation details. "entity": "entity", "mainAbbreviation": "LC", "name": "Leaf Color", - "ontologyRefernce": { + "ontologyReference": { "documentationLinks": [ { "URL": "https://ontology.org/t3", @@ -1928,7 +1988,7 @@ Call to retrieve a list of observationVariables available in the system. { "contextOfUse": [], "crop": "maize", - "date": "2018-12-04", + "date": "2018-12-05", "defaultValue": "10", "documentationURL": "https://brapi.org", "growthStage": "1", @@ -1941,7 +2001,7 @@ Call to retrieve a list of observationVariables available in the system. "methodDbId": "m1", "methodName": "Tape Measure", "name": "Tape Measure", - "ontologyRefernce": { + "ontologyReference": { "documentationLinks": [ { "URL": "https://ontology.org/m1", @@ -1960,7 +2020,7 @@ Call to retrieve a list of observationVariables available in the system. "observationVariableName": "Plant height", "ontologyDbId": "MO_123", "ontologyName": "Ontology.org", - "ontologyRefernce": { + "ontologyReference": { "documentationLinks": [ { "URL": "https://ontology.org", @@ -1976,7 +2036,7 @@ Call to retrieve a list of observationVariables available in the system. "dataType": "Numerical", "decimalPlaces": 1, "name": "Centimeter", - "ontologyRefernce": { + "ontologyReference": { "documentationLinks": [ { "URL": "https://ontology.org/s1", @@ -2009,7 +2069,7 @@ Call to retrieve a list of observationVariables available in the system. "entity": "entity", "mainAbbreviation": "H", "name": "Plant Height", - "ontologyRefernce": { + "ontologyReference": { "documentationLinks": [ { "URL": "https://ontology.org/t1", @@ -2032,7 +2092,7 @@ Call to retrieve a list of observationVariables available in the system. { "contextOfUse": [], "crop": "maize", - "date": "2018-12-04", + "date": "2018-12-05", "defaultValue": "10", "documentationURL": "https://brapi.org", "growthStage": "1", @@ -2045,7 +2105,7 @@ Call to retrieve a list of observationVariables available in the system. "methodDbId": "m3", "methodName": "Standard Color Palette", "name": "Standard Color Palette", - "ontologyRefernce": { + "ontologyReference": { "documentationLinks": [ { "URL": "https://ontology.org/m3", @@ -2064,7 +2124,7 @@ Call to retrieve a list of observationVariables available in the system. "observationVariableName": "Carotenoid", "ontologyDbId": "MO_123", "ontologyName": "Ontology.org", - "ontologyRefernce": { + "ontologyReference": { "documentationLinks": [ { "URL": "https://ontology.org", @@ -2080,7 +2140,7 @@ Call to retrieve a list of observationVariables available in the system. "dataType": "Nominal", "decimalPlaces": 0, "name": "Color", - "ontologyRefernce": { + "ontologyReference": { "documentationLinks": [ { "URL": "https://ontology.org/s3", @@ -2119,7 +2179,7 @@ Call to retrieve a list of observationVariables available in the system. "entity": "entity", "mainAbbreviation": "LC", "name": "Leaf Color", - "ontologyRefernce": { + "ontologyReference": { "documentationLinks": [ { "URL": "https://ontology.org/t3", @@ -2194,7 +2254,7 @@ Retrieve variable details "result": { "contextOfUse": [], "crop": "maize", - "date": "2018-12-04", + "date": "2018-12-05", "defaultValue": "10", "documentationURL": "https://brapi.org", "growthStage": "1", @@ -2207,7 +2267,7 @@ Retrieve variable details "methodDbId": "m1", "methodName": "Tape Measure", "name": "Tape Measure", - "ontologyRefernce": { + "ontologyReference": { "documentationLinks": [ { "URL": "https://ontology.org/m1", @@ -2226,7 +2286,7 @@ Retrieve variable details "observationVariableName": "Plant height", "ontologyDbId": "MO_123", "ontologyName": "Ontology.org", - "ontologyRefernce": { + "ontologyReference": { "documentationLinks": [ { "URL": "https://ontology.org", @@ -2242,7 +2302,7 @@ Retrieve variable details "dataType": "Numerical", "decimalPlaces": 1, "name": "Centimeter", - "ontologyRefernce": { + "ontologyReference": { "documentationLinks": [ { "URL": "https://ontology.org/s1", @@ -2275,7 +2335,7 @@ Retrieve variable details "entity": "entity", "mainAbbreviation": "H", "name": "Plant Height", - "ontologyRefernce": { + "ontologyReference": { "documentationLinks": [ { "URL": "https://ontology.org/t1", diff --git a/Specification/People/README.md b/Specification/People/README.md index d98243c5..3d19292e 100644 --- a/Specification/People/README.md +++ b/Specification/People/README.md @@ -139,7 +139,7 @@ Create a new person "lastName": "Smith", "mailingAddress": "string", "middleName": "string", - "personDbId": "5bf0f4b9-0e59-4265-88e2-ea2b589e3d2f", + "personDbId": "4f67d1b5-d95e-4bf5-b719-79a64b619f00", "phoneNumber": "string", "userID": "string" } diff --git a/Specification/Phenotypes/README.md b/Specification/Phenotypes/README.md index a90f2554..d6f2199c 100644 --- a/Specification/Phenotypes/README.md +++ b/Specification/Phenotypes/README.md @@ -914,7 +914,7 @@ Images can be optionally be uploaded using this call by providing a zipfile of a "result": { "observations": [ { - "observationDbId": "93f807fb-a07f-4882-9f8f-8a48302eee3b", + "observationDbId": "bb989815-86bf-430b-9d87-054df8919767", "observationUnitDbId": "1", "observationVariableDbId": "MO_123:100002" } @@ -1415,7 +1415,7 @@ See Search Services for additional implementation details. }, { "collector": "string", - "observationDbId": "93f807fb-a07f-4882-9f8f-8a48302eee3b", + "observationDbId": "bb989815-86bf-430b-9d87-054df8919767", "observationTimeStamp": "1970-01-18T14:02:52-05:00", "observationVariableDbId": "MO_123:100002", "observationVariableName": "Plant height", diff --git a/Specification/Samples/README.md b/Specification/Samples/README.md index 2d5c396d..30c80f05 100644 --- a/Specification/Samples/README.md +++ b/Specification/Samples/README.md @@ -312,8 +312,8 @@ Call to register the event of a sample being taken. Sample ID is assigned as a r "status": [] }, "result": { - "sampleDbId": "b528f627-7548-4d01-a3c2-6b78f9a4f221", - "sampleId": "b528f627-7548-4d01-a3c2-6b78f9a4f221" + "sampleDbId": "d3636ed9-f0d5-47fd-90ea-278d95043411", + "sampleId": "d3636ed9-f0d5-47fd-90ea-278d95043411" } } ``` diff --git a/Specification/Studies/README.md b/Specification/Studies/README.md index 019ae461..b26bc9ea 100644 --- a/Specification/Studies/README.md +++ b/Specification/Studies/README.md @@ -1454,8 +1454,8 @@ Refer to the data type definition of variables in `/Specification/ObservationVar "pagination": { "currentPage": 0, "pageSize": 2, - "totalCount": 0, - "totalPages": 0 + "totalCount": 5, + "totalPages": 3 }, "status": [] }, @@ -1464,7 +1464,7 @@ Refer to the data type definition of variables in `/Specification/ObservationVar { "contextOfUse": [], "crop": "maize", - "date": "2018-12-04", + "date": "2018-12-05", "defaultValue": "10", "documentationURL": "https://brapi.org", "growthStage": "1", @@ -1477,7 +1477,7 @@ Refer to the data type definition of variables in `/Specification/ObservationVar "methodDbId": "m1", "methodName": "string", "name": "string", - "ontologyRefernce": { + "ontologyReference": { "documentationLinks": [ { "URL": "string", @@ -1496,7 +1496,7 @@ Refer to the data type definition of variables in `/Specification/ObservationVar "observationVariableName": "Plant height", "ontologyDbId": "MO_123", "ontologyName": "Ontology.org", - "ontologyRefernce": { + "ontologyReference": { "documentationLinks": [ { "URL": "https://ontology.org", @@ -1512,7 +1512,7 @@ Refer to the data type definition of variables in `/Specification/ObservationVar "dataType": "Code", "decimalPlaces": 0, "name": "string", - "ontologyRefernce": { + "ontologyReference": { "documentationLinks": [ { "URL": "string", @@ -1549,7 +1549,7 @@ Refer to the data type definition of variables in `/Specification/ObservationVar "entity": "string", "mainAbbreviation": "string", "name": "string", - "ontologyRefernce": { + "ontologyReference": { "documentationLinks": [ { "URL": "string", @@ -1574,7 +1574,7 @@ Refer to the data type definition of variables in `/Specification/ObservationVar { "contextOfUse": [], "crop": "maize", - "date": "2018-12-04", + "date": "2018-12-05", "defaultValue": "10", "documentationURL": "https://brapi.org", "growthStage": "1", @@ -1587,7 +1587,7 @@ Refer to the data type definition of variables in `/Specification/ObservationVar "methodDbId": "m3", "methodName": "Standard Color Palette", "name": "Standard Color Palette", - "ontologyRefernce": { + "ontologyReference": { "documentationLinks": [ { "URL": "https://ontology.org/m3", @@ -1606,7 +1606,7 @@ Refer to the data type definition of variables in `/Specification/ObservationVar "observationVariableName": "Carotenoid", "ontologyDbId": "MO_123", "ontologyName": "Ontology.org", - "ontologyRefernce": { + "ontologyReference": { "documentationLinks": [ { "URL": "https://ontology.org", @@ -1622,7 +1622,7 @@ Refer to the data type definition of variables in `/Specification/ObservationVar "dataType": "Nominal", "decimalPlaces": 0, "name": "Color", - "ontologyRefernce": { + "ontologyReference": { "documentationLinks": [ { "URL": "https://ontology.org/s3", @@ -1661,7 +1661,7 @@ Refer to the data type definition of variables in `/Specification/ObservationVar "entity": "entity", "mainAbbreviation": "LC", "name": "Leaf Color", - "ontologyRefernce": { + "ontologyReference": { "documentationLinks": [ { "URL": "https://ontology.org/t3", @@ -1680,324 +1680,6 @@ Refer to the data type definition of variables in `/Specification/ObservationVar "xref": "xref" }, "xref": "MO_123:100003" - }, - { - "contextOfUse": [], - "crop": "maize", - "date": "2018-12-04", - "defaultValue": "10", - "documentationURL": "https://brapi.org", - "growthStage": "1", - "institution": "1", - "language": "English", - "method": { - "class": "Numeric", - "description": "Dried sample on electric scale", - "formula": "NA", - "methodDbId": "m2", - "methodName": "Dry Electric Scale", - "name": "Dry Electric Scale", - "ontologyRefernce": { - "documentationLinks": [ - { - "URL": "https://ontology.org/m2", - "type": "WEBPAGE", - "url": "https://ontology.org/m2" - } - ], - "ontologyDbId": "MO_123", - "ontologyName": "Ontology.org", - "version": "17" - }, - "reference": "google.com" - }, - "name": "Root weight", - "observationVariableDbId": "MO_123:100004", - "observationVariableName": "Root weight", - "ontologyDbId": "MO_123", - "ontologyName": "Ontology.org", - "ontologyRefernce": { - "documentationLinks": [ - { - "URL": "https://ontology.org", - "type": "WEBPAGE", - "url": "https://ontology.org" - } - ], - "ontologyDbId": "MO_123", - "ontologyName": "Ontology.org", - "version": "17" - }, - "scale": { - "dataType": "Numerical", - "decimalPlaces": 3, - "name": "Kilogram", - "ontologyRefernce": { - "documentationLinks": [ - { - "URL": "https://ontology.org/s2", - "type": "RDF", - "url": "https://ontology.org/s2" - } - ], - "ontologyDbId": "MO_123", - "ontologyName": "Ontology.org", - "version": "17" - }, - "scaleDbId": "s2", - "scaleName": "Kilogram", - "validValues": { - "categories": [], - "max": 99999, - "min": 0 - }, - "xref": "xref" - }, - "scientist": "Bob", - "status": "active", - "submissionTimestamp": "2011-06-14T22:12:51-04:00", - "synonyms": [], - "trait": { - "alternativeAbbreviations": [], - "attribute": "root weight", - "class": "Numeric", - "description": "root weight", - "entity": "entity", - "mainAbbreviation": "RW", - "name": "Root Weight", - "ontologyRefernce": { - "documentationLinks": [ - { - "URL": "https://ontology.org/t2", - "type": "OBO", - "url": "https://ontology.org/t2" - } - ], - "ontologyDbId": "MO_123", - "ontologyName": "Ontology.org", - "version": "17" - }, - "status": "active", - "synonyms": [], - "traitDbId": "t2", - "traitName": "Root Weight", - "xref": "xref" - }, - "xref": "MO_123:100004" - }, - { - "contextOfUse": [], - "crop": "maize", - "date": "2018-12-04", - "defaultValue": "10", - "documentationURL": "https://brapi.org", - "growthStage": "1", - "institution": "1", - "language": "English", - "method": { - "class": "Categorical", - "description": "Comparing sample color to standard color palette", - "formula": "NA", - "methodDbId": "m3", - "methodName": "Standard Color Palette", - "name": "Standard Color Palette", - "ontologyRefernce": { - "documentationLinks": [ - { - "URL": "https://ontology.org/m3", - "type": "OBO", - "url": "https://ontology.org/m3" - } - ], - "ontologyDbId": "MO_123", - "ontologyName": "Ontology.org", - "version": "17" - }, - "reference": "google.com" - }, - "name": "Root color", - "observationVariableDbId": "MO_123:100005", - "observationVariableName": "Root color", - "ontologyDbId": "MO_123", - "ontologyName": "Ontology.org", - "ontologyRefernce": { - "documentationLinks": [ - { - "URL": "https://ontology.org", - "type": "WEBPAGE", - "url": "https://ontology.org" - } - ], - "ontologyDbId": "MO_123", - "ontologyName": "Ontology.org", - "version": "17" - }, - "scale": { - "dataType": "Nominal", - "decimalPlaces": 0, - "name": "Color", - "ontologyRefernce": { - "documentationLinks": [ - { - "URL": "https://ontology.org/s3", - "type": "WEBPAGE", - "url": "https://ontology.org/s3" - } - ], - "ontologyDbId": "MO_123", - "ontologyName": "Ontology.org", - "version": "17" - }, - "scaleDbId": "s3", - "scaleName": "Color", - "validValues": { - "categories": [ - "dark red", - "red", - "dark blue", - "blue", - "black" - ], - "max": 0, - "min": 0 - }, - "xref": "xref" - }, - "scientist": "Bob", - "status": "active", - "submissionTimestamp": "2011-06-14T22:12:51-04:00", - "synonyms": [], - "trait": { - "alternativeAbbreviations": [], - "attribute": "root color", - "class": "Categorical", - "description": "color of root sample", - "entity": "entity", - "mainAbbreviation": "RC", - "name": "Root Color", - "ontologyRefernce": { - "documentationLinks": [ - { - "URL": "https://ontology.org/t4", - "type": "WEBPAGE", - "url": "https://ontology.org/t4" - } - ], - "ontologyDbId": "MO_123", - "ontologyName": "Ontology.org", - "version": "17" - }, - "status": "active", - "synonyms": [], - "traitDbId": "t4", - "traitName": "Root Color", - "xref": "xref" - }, - "xref": "MO_123:100005" - }, - { - "contextOfUse": [], - "crop": "maize", - "date": "2018-12-04", - "defaultValue": "10", - "documentationURL": "https://brapi.org", - "growthStage": "1", - "institution": "1", - "language": "English", - "method": { - "class": "Percentage", - "description": "Image analysis of sample photo", - "formula": "Bobs Color Threshold Tool", - "methodDbId": "m4", - "methodName": "Image analysis", - "name": "Image analysis", - "ontologyRefernce": { - "documentationLinks": [ - { - "URL": "https://ontology.org/m4", - "type": "RDF", - "url": "https://ontology.org/m4" - } - ], - "ontologyDbId": "MO_123", - "ontologyName": "Ontology.org", - "version": "17" - }, - "reference": "https://bobsimageanalysis.com" - }, - "name": "Virus severity", - "observationVariableDbId": "MO_123:100006", - "observationVariableName": "Virus severity", - "ontologyDbId": "MO_123", - "ontologyName": "Ontology.org", - "ontologyRefernce": { - "documentationLinks": [ - { - "URL": "https://ontology.org", - "type": "WEBPAGE", - "url": "https://ontology.org" - } - ], - "ontologyDbId": "MO_123", - "ontologyName": "Ontology.org", - "version": "17" - }, - "scale": { - "dataType": "Numerical", - "decimalPlaces": 0, - "name": "Percentage", - "ontologyRefernce": { - "documentationLinks": [ - { - "URL": "https://ontology.org/s4", - "type": "OBO", - "url": "https://ontology.org/s4" - } - ], - "ontologyDbId": "MO_123", - "ontologyName": "Ontology.org", - "version": "17" - }, - "scaleDbId": "s4", - "scaleName": "Percentage", - "validValues": { - "categories": [], - "max": 100, - "min": 0 - }, - "xref": "xref" - }, - "scientist": "Bob", - "status": "active", - "submissionTimestamp": "2011-06-14T22:12:51-04:00", - "synonyms": [], - "trait": { - "alternativeAbbreviations": [], - "attribute": "Virus severity", - "class": "Percentage", - "description": "Percentage of contaminated sample", - "entity": "entity", - "mainAbbreviation": "LC", - "name": "Virus severity", - "ontologyRefernce": { - "documentationLinks": [ - { - "URL": "https://ontology.org/t5", - "type": "OBO", - "url": "https://ontology.org/t5" - } - ], - "ontologyDbId": "MO_123", - "ontologyName": "Ontology.org", - "version": "17" - }, - "status": "active", - "synonyms": [], - "traitDbId": "t5", - "traitName": "Virus severity", - "xref": "xref" - }, - "xref": "MO_123:100006" } ], "studyDbId": "1001", @@ -2218,7 +1900,7 @@ Implementation Guidelines: "observationVariableDbId": "MO_123:100004" }, { - "observationDbId": "f9b1cc8a-6f3f-4032-b199-52a9d752c6f5", + "observationDbId": "1f55443e-c7e1-4b71-bc9c-02ddbca9ab7d", "observationUnitDbId": "11", "observationVariableDbId": "MO_123:100002" } @@ -2337,7 +2019,7 @@ The main API call for field data collection, to retrieve all the observation uni }, { "collector": "string", - "observationDbId": "93f807fb-a07f-4882-9f8f-8a48302eee3b", + "observationDbId": "bb989815-86bf-430b-9d87-054df8919767", "observationTimeStamp": "1970-01-18T14:02:52-05:00", "observationVariableDbId": "MO_123:100002", "observationVariableName": "Plant height", @@ -2789,8 +2471,8 @@ Implementation Guidelines: "result": { "observations": [ { - "observationDbId": "06d16532-e532-4073-b2c1-d2c50472bb22", - "observationUnitDbId": "a3c304d2-1929-429f-b043-b8d3abbb5203", + "observationDbId": "f439cdc6-768f-4d11-b66c-489d980b3d3b", + "observationUnitDbId": "ee89a58d-b104-437b-9cb4-7b500eaafa11", "observationVariableDbId": "MO_123:100002" } ] @@ -3040,8 +2722,8 @@ test-server.brapi.org/brapi/v1/studies/{studyDbId}/observationVariables "pagination": { "currentPage": 0, "pageSize": 0, - "totalCount": 0, - "totalPages": 0 + "totalCount": 5, + "totalPages": 1 }, "status": [] }, @@ -3050,7 +2732,7 @@ test-server.brapi.org/brapi/v1/studies/{studyDbId}/observationVariables { "contextOfUse": [], "crop": "maize", - "date": "2018-12-04", + "date": "2018-12-05", "defaultValue": "10", "documentationURL": "https://brapi.org", "growthStage": "1", @@ -3063,7 +2745,7 @@ test-server.brapi.org/brapi/v1/studies/{studyDbId}/observationVariables "methodDbId": "m1", "methodName": "string", "name": "string", - "ontologyRefernce": { + "ontologyReference": { "documentationLinks": [ { "URL": "string", @@ -3082,7 +2764,7 @@ test-server.brapi.org/brapi/v1/studies/{studyDbId}/observationVariables "observationVariableName": "Plant height", "ontologyDbId": "MO_123", "ontologyName": "Ontology.org", - "ontologyRefernce": { + "ontologyReference": { "documentationLinks": [ { "URL": "https://ontology.org", @@ -3098,7 +2780,7 @@ test-server.brapi.org/brapi/v1/studies/{studyDbId}/observationVariables "dataType": "Code", "decimalPlaces": 0, "name": "string", - "ontologyRefernce": { + "ontologyReference": { "documentationLinks": [ { "URL": "string", @@ -3135,7 +2817,7 @@ test-server.brapi.org/brapi/v1/studies/{studyDbId}/observationVariables "entity": "string", "mainAbbreviation": "string", "name": "string", - "ontologyRefernce": { + "ontologyReference": { "documentationLinks": [ { "URL": "string", @@ -3160,7 +2842,7 @@ test-server.brapi.org/brapi/v1/studies/{studyDbId}/observationVariables { "contextOfUse": [], "crop": "maize", - "date": "2018-12-04", + "date": "2018-12-05", "defaultValue": "10", "documentationURL": "https://brapi.org", "growthStage": "1", @@ -3173,7 +2855,7 @@ test-server.brapi.org/brapi/v1/studies/{studyDbId}/observationVariables "methodDbId": "m3", "methodName": "Standard Color Palette", "name": "Standard Color Palette", - "ontologyRefernce": { + "ontologyReference": { "documentationLinks": [ { "URL": "https://ontology.org/m3", @@ -3192,7 +2874,7 @@ test-server.brapi.org/brapi/v1/studies/{studyDbId}/observationVariables "observationVariableName": "Carotenoid", "ontologyDbId": "MO_123", "ontologyName": "Ontology.org", - "ontologyRefernce": { + "ontologyReference": { "documentationLinks": [ { "URL": "https://ontology.org", @@ -3208,7 +2890,7 @@ test-server.brapi.org/brapi/v1/studies/{studyDbId}/observationVariables "dataType": "Nominal", "decimalPlaces": 0, "name": "Color", - "ontologyRefernce": { + "ontologyReference": { "documentationLinks": [ { "URL": "https://ontology.org/s3", @@ -3247,7 +2929,7 @@ test-server.brapi.org/brapi/v1/studies/{studyDbId}/observationVariables "entity": "entity", "mainAbbreviation": "LC", "name": "Leaf Color", - "ontologyRefernce": { + "ontologyReference": { "documentationLinks": [ { "URL": "https://ontology.org/t3", @@ -3270,7 +2952,7 @@ test-server.brapi.org/brapi/v1/studies/{studyDbId}/observationVariables { "contextOfUse": [], "crop": "maize", - "date": "2018-12-04", + "date": "2018-12-05", "defaultValue": "10", "documentationURL": "https://brapi.org", "growthStage": "1", @@ -3283,7 +2965,7 @@ test-server.brapi.org/brapi/v1/studies/{studyDbId}/observationVariables "methodDbId": "m2", "methodName": "Dry Electric Scale", "name": "Dry Electric Scale", - "ontologyRefernce": { + "ontologyReference": { "documentationLinks": [ { "URL": "https://ontology.org/m2", @@ -3302,7 +2984,7 @@ test-server.brapi.org/brapi/v1/studies/{studyDbId}/observationVariables "observationVariableName": "Root weight", "ontologyDbId": "MO_123", "ontologyName": "Ontology.org", - "ontologyRefernce": { + "ontologyReference": { "documentationLinks": [ { "URL": "https://ontology.org", @@ -3318,7 +3000,7 @@ test-server.brapi.org/brapi/v1/studies/{studyDbId}/observationVariables "dataType": "Numerical", "decimalPlaces": 3, "name": "Kilogram", - "ontologyRefernce": { + "ontologyReference": { "documentationLinks": [ { "URL": "https://ontology.org/s2", @@ -3351,7 +3033,7 @@ test-server.brapi.org/brapi/v1/studies/{studyDbId}/observationVariables "entity": "entity", "mainAbbreviation": "RW", "name": "Root Weight", - "ontologyRefernce": { + "ontologyReference": { "documentationLinks": [ { "URL": "https://ontology.org/t2", @@ -3374,7 +3056,7 @@ test-server.brapi.org/brapi/v1/studies/{studyDbId}/observationVariables { "contextOfUse": [], "crop": "maize", - "date": "2018-12-04", + "date": "2018-12-05", "defaultValue": "10", "documentationURL": "https://brapi.org", "growthStage": "1", @@ -3387,7 +3069,7 @@ test-server.brapi.org/brapi/v1/studies/{studyDbId}/observationVariables "methodDbId": "m3", "methodName": "Standard Color Palette", "name": "Standard Color Palette", - "ontologyRefernce": { + "ontologyReference": { "documentationLinks": [ { "URL": "https://ontology.org/m3", @@ -3406,7 +3088,7 @@ test-server.brapi.org/brapi/v1/studies/{studyDbId}/observationVariables "observationVariableName": "Root color", "ontologyDbId": "MO_123", "ontologyName": "Ontology.org", - "ontologyRefernce": { + "ontologyReference": { "documentationLinks": [ { "URL": "https://ontology.org", @@ -3422,7 +3104,7 @@ test-server.brapi.org/brapi/v1/studies/{studyDbId}/observationVariables "dataType": "Nominal", "decimalPlaces": 0, "name": "Color", - "ontologyRefernce": { + "ontologyReference": { "documentationLinks": [ { "URL": "https://ontology.org/s3", @@ -3461,7 +3143,7 @@ test-server.brapi.org/brapi/v1/studies/{studyDbId}/observationVariables "entity": "entity", "mainAbbreviation": "RC", "name": "Root Color", - "ontologyRefernce": { + "ontologyReference": { "documentationLinks": [ { "URL": "https://ontology.org/t4", @@ -3484,7 +3166,7 @@ test-server.brapi.org/brapi/v1/studies/{studyDbId}/observationVariables { "contextOfUse": [], "crop": "maize", - "date": "2018-12-04", + "date": "2018-12-05", "defaultValue": "10", "documentationURL": "https://brapi.org", "growthStage": "1", @@ -3497,7 +3179,7 @@ test-server.brapi.org/brapi/v1/studies/{studyDbId}/observationVariables "methodDbId": "m4", "methodName": "Image analysis", "name": "Image analysis", - "ontologyRefernce": { + "ontologyReference": { "documentationLinks": [ { "URL": "https://ontology.org/m4", @@ -3516,7 +3198,7 @@ test-server.brapi.org/brapi/v1/studies/{studyDbId}/observationVariables "observationVariableName": "Virus severity", "ontologyDbId": "MO_123", "ontologyName": "Ontology.org", - "ontologyRefernce": { + "ontologyReference": { "documentationLinks": [ { "URL": "https://ontology.org", @@ -3532,7 +3214,7 @@ test-server.brapi.org/brapi/v1/studies/{studyDbId}/observationVariables "dataType": "Numerical", "decimalPlaces": 0, "name": "Percentage", - "ontologyRefernce": { + "ontologyReference": { "documentationLinks": [ { "URL": "https://ontology.org/s4", @@ -3565,7 +3247,7 @@ test-server.brapi.org/brapi/v1/studies/{studyDbId}/observationVariables "entity": "entity", "mainAbbreviation": "LC", "name": "Virus severity", - "ontologyRefernce": { + "ontologyReference": { "documentationLinks": [ { "URL": "https://ontology.org/t5",