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Eventually these services will be HTTPS only and disallow HTTP. Users will pass something like ?access_token=... as a query parameter for every request to the service

...

Query API

...

Examples

...

This is a REST api (see Service API Design for more details as to what this means). You can create entities, updated entities, read entities, and delete entities. More advanced querying will be implemented as a separate API. Partial updates (e.g., just updating two fields in a dataset) are not supported. In a nutshell, when you update something like a dataset, you GET the dataset first, modify the properties you want to change, and then send the entire object back to the service so that this revised entity overwrites the previously stored entity.

The layer preview info in the dataset examples is out of date. It will be updated soon. Just use curl against the live service to see the current format.

Get Datasets

Optional Parameters

  • offset - integer - 1-based pagination offset
  • limit - integer - maximum number of results to return
  • sort - string - the name of the primary field upon which to sort
  • ascending - boolean - whether or not to sort ascending

Request

Code Block

curl -i -H Accept:application/json "http://deflaux-test.appspot.com/repo/v1/dataset?limit=3"

Response

...

'Select *' Query

Right now only a subset of query functionality is supported

Code Block
SELECT * FROM <data type> [LIMIT <#>] [OFFSET <#>]

Request

Code Block
curl -i -H Accept:application/json 'http://deflaux-test.appspot.com/repo/v1/query?query=select+*+from+dataset+limit+3+offset+1'

Response

Code Block

HTTP/1.1 200 OK
Content-Type: application/json
Date: Sun, 13 Feb 2011 00:27:40 GMT
Server: Google Frontend
Cache-Control: private, x-gzip-ok=""
Transfer-Encoding: chunked

{
  "results": [
    {
      "Disease": ["Cancer"],
      "Institution": ["TCGA"],
      {"Number          "nameof Samples":"Pediatric AML TARGET" ["465"],
      "Reference / PubMed "annotationsID":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYgvcCDA/annotations",
   ["18772890"],
      "idSpecies": ["agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYgvcCDAHuman"],
      "Tumor / Tissue "versionType":"0.0.1" ["Glioblastoma"],
      "creationDate": 1297465568905,
      "descriptioncreator": null,
      "description": null,
      "statushasClinicalData":"In Transition"false,
         "urihasExpressionData":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYgvcCDA",
   false,
      "etaghasGeneticData":"1703131409" false,
         "creatorid": "Soheil MeshinchiagxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQY8aIEDA",
         "creationDatename":1296182253120, "Glioblastoma  TCGA",
      "releaseDate": null,
 
       "layerstatus":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYgvcCDA/layer",
 "Available",
        "hasExpressionDataversion":true,
 "0.0.1"
      },
 "hasGeneticData":false,   {
      "hasClinicalDataDisease":false
      } ["Metabolic"],
      {
"Institution": ["UCLA"],
      "Number of Samples"name":"Flint HS Mice" ["111"],
      "Reference / PubMed ID"annotations":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQY2q0DDA/annotations",
 ["12646919"],
        "idSpecies": ["agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQY2q0DDAMouse"],
      "Tumor / Tissue Type"version":"0.0.1",
  ["Liver"],
       "descriptioncreationDate":null 1297465572211,
 
       "statuscreator": "FutureJake Lusis",
      "description": null,
      "urihasClinicalData":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQY2q0DDA", false,
      "hasExpressionData": false,
      "etaghasGeneticData":"1025901212",
   false,
      "creatorid": "Jonathan FlintagxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQY2aoEDA",
         "creationDatename":1296182255070, "Mouse Model of Diet-Induced Atherosclerosis",
      "releaseDate": null,
         "layer":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQY2q0DDA/layer"status": "Available",
         "hasExpressionDataversion":true,
 "0.0.1"
    },
   "hasGeneticData":true, {
        "hasClinicalDataDisease":true ["Cancer"],
     }, "Institution": ["BCCA Cambridge"],
   {   "Number of      "name":"Glioblastoma TCGA"Samples": ["1500"],
         "annotationsSpecies":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYseQDDA/annotations" ["Human"],
      "Tumor / Tissue "idType": ["agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYseQDDABreast"],
      "creationDate": 1297465580576,
      "versioncreator":"0.0.1 "Aparicio, Caldas",
  
      "description": null,
 
       "statushasClinicalData":"Available" false,
         "urihasExpressionData":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYseQDDA",
  false,
       "etaghasGeneticData":"456728335" false,
        "id": "creatoragxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQY2qoEDA":null,
 
       "creationDatename":1296182238229, "METABRIC Breast Cancer",
      "releaseDate": null,

        "layerstatus":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYseQDDA/layer",
  "In Transition",
       "hasExpressionDataversion":false,
 "0.0.1"
    }
   "hasGeneticData":false,
      ],
  "hasClinicalDatatotalNumberOfResults":false 11
}

'Order By' Query

Right now only a subset of query functionality is supported

Code Block
SELECT * FROM <data type> }ORDER BY "<field name>" [ASC|DESC], [LIMIT <#>]  "totalNumberOfResults":10,
   "paging":{
      "next":"/repo/v1/dataset?offset=4&limit=3"
   }
}

Get a Dataset

Request

Code Block

curl -i -H Accept:application/json "[OFFSET #]

Request

Code Block
curl -i -H Accept:application/json 'http://deflaux-test.appspot.com/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYseQDDA"
query?query=select+*+from+dataset+order+by+"name"+limit+3+offset+1'

Response

Code Block
HTTP/1.1 200 OK
ETag: 456728335
Content-Type: application/json
Date: TueSun, 0113 Feb 2011 1800:2227:2441 GMT
Server: Google Frontend
Cache-Control: private, x-gzip-ok=""
Transfer-Encoding: chunked

{
   "nameresults":"Glioblastoma TCGA",
   "annotations":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYseQDDA/annotations", [
    {
      "idDate Curated":"agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYseQDDA", [1296432000000],
      "versionDisease":"0.0.1" ["Imaginary Friends"],
   "description":null,    "statusInstitution": ["AvailableSage Bionetworks"],
   "uri   "Number of Samples":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYseQDDA", ["42"],
      "etagSpecies": ["456728335Unicorn"],
   "creator":null,
   "creationDate":1296182238229   "Tumor / Tissue Type": ["Unicorn Horn"],
   "releaseDate":null,    "layerscreationDate":[ 1297465586365,
     { "creator": "Nicole Deflaux",
      "iddescription":"agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYAQw",
   null,
      "typehasClinicalData":"C",
   false,
      "urihasExpressionData":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYseQDDA/layer/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYAQw"
 false,
     }, "hasGeneticData": false,
    {  "id": "agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQY4dEEDA",
      "idname": "agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYiaECDAFake Dataset",

        "typereleaseDate":"E",
   1297382400000,
      "uristatus":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYseQDDA/layer/agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYiaECDA" "Never",
      },
"version": "0.0.1"
    },
 {   {
      "idDisease": ["agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYmfIBDANormal Phenotypes"],
      "Number of  "typeSamples": ["G1027"],
         "uriSpecies":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYseQDDA/layer/agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYmfIBDA" ["Mouse"],
      "creationDate": 1297465585103,
}    ] }

Get Annotations for a Dataset

Request

Code Block

curl -i -H Accept:application/json "http://deflaux-test.appspot.com/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYseQDDA/annotations"

Response

Code Block

HTTP/1.1 200 OK
ETag: -1919132670
Content-Type: application/json
Date: Tue, 01 Feb 2011 18:24:15 GMT
Server: Google Frontend
Cache-Control: private, x-gzip-ok=""
Transfer-Encoding: chunked

{ "creator": "Jonathan Flint",
      "description": null,
      "hasClinicalData": false,
      "hasExpressionData": false,
      "hasGeneticData": false,
      "id": "agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYseQDDAagxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYksIEDA",
      "uriname":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYseQDDA/annotations "Flint HS Mice",
   "etag":"-1919132670",
   "creationDatereleaseDate": null,
      "stringAnnotationsstatus":{ "Future",
      "Diseaseversion":[ "0.0.1"
    },
    {
"Cancer"      "Disease": ["Cancer"],
      "Tumor / Tissue TypeInstitution": ["TCGA"],
      "Number of Samples": ["Glioblastoma465"],
      "Reference / PubMed ID": ["18772890"],
      "Species": ["Human"],
      "Tumor / Tissue Type": ["HumanGlioblastoma"],
      ]"creationDate": 1297465568905,
      "Institutioncreator":[ null,
      "description": null,
"TCGA"      "hasClinicalData": ]false,
      "Reference / PubMed IDhasExpressionData":[ false,
        "18772890hasGeneticData": false,
    ]    },
   "floatAnnotations":{"id": "agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQY8aIEDA",
      "Number of Samples":[name": "Glioblastoma TCGA",
      "releaseDate": null,
 465.0     "status": "Available",
]    },   "version": "dateAnnotations":{0.0.1"
    }
 }

Create a Dataset

...

 ],
  "totalNumberOfResults": 11
}

'Where Equal To' Query

Right now only a subset of query functionality is supported

Code Block
SELECT curl* -iFROM -H Accept:application/json -H Content-Type:application/json
-d '{"name":"test dataset", "creator":"fake creator", "releaseDate":"2009-10-01", "status":"not curated"}'
http://localhost:8080/repo/v1/dataset

Response

Code Block

HTTP/1.1 201 Created
ETag: 1736839268
Location: /repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYBAw<data type> WHERE "<field name>" == "<value>" [LIMIT <#>] [OFFSET #]

Request

Code Block
curl -i -H Accept:application/json 'http://deflaux-test.appspot.com/repo/v1/query?query=select+*+from+dataset+where+"Species"+==+"Human"+limit+3+offset+1'

Response

Code Block

HTTP/1.1 200 OK
Content-Type: application/json
Transfer-EncodingDate: chunked
Server: Jetty(6.1.x)

{
   "name":"test dataset",
   "annotations":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYAQw/annotations",Sun, 13 Feb 2011 00:27:43 GMT
Server: Google Frontend
Cache-Control: private, x-gzip-ok=""
Transfer-Encoding: chunked

{
  "results": [
    {
      "idDisease": ["agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYAQwCancer"],
      "versionInstitution":"0.0.1" ["TCGA"],
   "creator   "Number of Samples": ["fake creator465"],

  "description":null,    "creationDate":1296595870715,Reference / PubMed  "statusID": ["not curated18772890"],
      "uriSpecies":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYAQw", ["Human"],
     "etag "Tumor / Tissue Type": ["1309185941Glioblastoma"],
      "releaseDatecreationDate":1254355200000 1297465568905,
   "layers":[] }

Update a Dataset

Note that in the example below the creator and description fields have been changed but all others remain the same.

Request:

Code Block

curl -i -H Accept:application/json -H Content-Type:application/json -X PUT -H ETag:1309185941 -d '{"creator": null,
      "description": null,
      "namehasClinicalData":"test dataset"false,
   "annotations":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYAQw/annotations"   "hasExpressionData": false,
      "idhasGeneticData":"agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYAQw" false,
      "versionid": "0.0.1agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQY8aIEDA",
      "creatorname": "updatedGlioblastoma creatorTCGA",
      "descriptionreleaseDate":"I just added a description" null,
   "creationDate":1296595870715,    "status": "not curatedAvailable",
   "uri":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYAQw",
   "etagversion": "1309185941",0.0.1"
    "releaseDate":1254355200000,},
    {
      "layersDisease": ["Cancer"],
}
' http://localhost:8080/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYAQw

Response

Code Block
 HTTP/1.1 200 OK ETag"Institution": -852418664
Content-Type: application/json
Transfer-Encoding: chunked
Server: Jetty(6.1.x)

{
   "name":"test dataset",["BCCA Cambridge"],
      "Number of Samples": ["1500"],
      "annotationsSpecies":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYAQw/annotations" ["Human"],
   "id   "Tumor / Tissue Type": ["agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYAQwBreast"],
      "versioncreationDate":"0.0.1" 1297465580576,
      "creator": "updatedAparicio, creatorCaldas",
      "description":"I justnull,
added a description",    "creationDatehasClinicalData":1296595870715 false,
      "statushasExpressionData":"not curated"false,
      "urihasGeneticData":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYAQw" false,
      "etagid": "-852418664agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQY2qoEDA",
      "releaseDatename":1254355200000 "METABRIC Breast Cancer",
      "layersreleaseDate":[] null,
}

Add Annotations to a Dataset

First get the empty annotations container for your newly created dataset

Request

Code Block
 curl -i -H Accept:application/json http://localhost:8080/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYAQw/annotations

Response

Code Block

HTTP/1.1 200 OK
ETag: 923521
Content-Type: application/json
Transfer-Encoding: chunked
Server: Jetty(6.1.x)

{
   "id":"agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYAQw",
   "creationDate":null, "status": "In Transition",
      "version": "0.0.1"
    },
    {
      "uriDisease":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYAQw/annotations", ["Cancer"],
      "etagInstitution": ["923521FHCRC"],
   "stringAnnotations   "Number of Samples":{

 ["200"],
  },    "floatAnnotationsSpecies":{

 ["Human"],
  },    "dateAnnotations":{Tumor / Tissue Type":  }
}

Then you add/modify the annotations of interest and do a PUT. Note that annotation values must always be list values even if the list is only of length one.

Request

Code Block

curl -i -H Accept:application/json -H Content-Type:application/json -X PUT -H ETag:923521 -d '{
   "id":"agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYAQw",
   "creationDate":["AML (pediatric)"],
      "creationDate": 1297465583813,
      "creator": "Soheil Meshinchi",
      "description": null,
      "urihasClinicalData":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYAQw/annotations" false,
      "etaghasExpressionData":"923521", false,
      "stringAnnotationshasGeneticData":{ false,
       "Experimental Design Templatesid":[ "exp-122887agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQY26oEDA",
"exp-97765"]
   },    "floatAnnotationsname":{ "Pediatric AML TARGET",
      "Number of SamplesreleaseDate":[500] null,
  },    "dateAnnotationsstatus":{ "In Transition",
      "Publication Dateversion":["2011-01-15"] "0.0.1"
    }
 }' http://localhost:8080 ],
  "totalNumberOfResults": 11
}

REST API Examples (Read Only)

Sanity check request

This is just a 'hello world' type request that you can make to ensure that the service is running.

Request

Code Block
curl -i -H Accept:application/json 'http://deflaux-test.appspot.com/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYAQw/annotations
test'

Response

Code Block
HTTP/1.1 200 OK
ETagContent-Language: en-1638393853US
Content-Type: application/json; Transfer-Encoding: chunked
Server: Jetty(6.1.x)

{
   "id":"agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYBww",
   "creationDate":null,
   "uri":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYBww/annotations",
   "etag":"-1638393853",
   "stringAnnotations":{
      "Experimental Design Templates":[
         "exp-122887",
         "exp-97765"
      ]
   },
   "floatAnnotations":{
      "Number of Samples":[
         500.0
      ]
   },
   "dateAnnotations":{charset=UTF-8
Pragma: no-cache
Cache-Control: no-cache, no-store, max-age=0
Expires: Thu, 01 Jan 1970 00:00:00 GMT
Date: Sun, 13 Feb 2011 00:27:43 GMT
Server: Google Frontend
Transfer-Encoding: chunked

{"hello": "REST for Datasets rocks"}

Get All Datasets

Optional Parameters

  • offset - integer - 1-based pagination offset
  • limit - integer - maximum number of results to return
  • sort - string - the name of the field upon which to sort
  • ascending - boolean - whether or not to sort ascending

Request

Code Block
curl -i -H Accept:application/json 'http://deflaux-test.appspot.com/repo/v1/dataset?sort=name&limit=3'

Response

Code Block

HTTP/1.1 200 OK
Content-Type: application/json
Date: Sun, 13 Feb 2011 00:27:44 GMT
Server: Google Frontend
Cache-Control: private, x-gzip-ok=""
Transfer-Encoding: chunked

{
  "paging": {"next": "/repo/v1/dataset?offset=4&limit=3&sort=name&ascending=true"},
  "results": [
    {
      "annotations": "/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQY4dEEDA/annotations",
      "Publication DatecreationDate":[ 1297465586365,
      "creator": "Nicole 1295049600000Deflaux",
      ]
"description": null,
  } }

Delete a Dataset

Request

Code Block

curl -i -X DELETE http://localhost:8080/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYAQw

Response

Code Block

HTTP/1.1 204 No Content
Server: Jetty(6.1.x)

Get a Layers for a Dataset

Request

Code Block

curl -i -H Accept:application/json http://localhost:8080/ "etag": "-1441125823",
      "hasClinicalData": false,
      "hasExpressionData": false,
      "hasGeneticData": false,
      "id": "agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQY4dEEDA",
      "layer": "/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUwwagxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQY4dEEDA/layer

Response

Code Block

HTTP/1.1 200 OK
Content-Type: application/json
Transfer-Encoding: chunked
Server: Jetty(6.1.x)

{",
      "name": "Fake Dataset",
      "resultsreleaseDate":[ 1297382400000,
     {
         "name"status":"Flint HS Mice Affy "Never",
 
       "annotationsuri": "/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww/layer/agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww/annotationsagxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQY4dEEDA",

        "idversion": "agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww0.0.1",
    },
    "type":"E",{
         "versionannotations":"0.0.1 "/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYksIEDA/annotations",
         "descriptioncreationDate":"this is a description",
  1297465585103,
       "creationDatecreator":1296690778880, "Jonathan Flint",
       "uridescription":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww/layer/agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww" null,
         "etag": "14247719251698149418",
         "publicationDatehasClinicalData":null false,
         "releaseNoteshasExpressionData":"this is a release note",
 false,
        "tissueTypehasGeneticData":"liver" false,
      "id":   "platformagxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYksIEDA":null,
      "layer":   "processingFacility":null,
 "/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYksIEDA/layer",
       "qcByname":null, "Flint HS Mice",
      "qcDatereleaseDate": null,
      }"status": "Future",
      {
 "uri": "/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYksIEDA",
       "nameversion":"Flint HS Mice Phenotypes", "0.0.1"
    },
    {
      "annotations": "/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww/layeragxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQY8aIEDA/agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjpBww/annotations",
         "idcreationDate":"agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjpBww" 1297465568905,
      "creator": null,
      "description": null,
      "typeetag": "C2011502454",
 
       "versionhasClinicalData":"0.0.1" false,
      "hasExpressionData": false,
 "description":"this is a description",  "hasGeneticData": false,
      "creationDateid":1296693007167 "agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQY8aIEDA",
         "urilayer": "/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUwwagxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQY8aIEDA/layer/agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjpBww",
 
       "etagname": "1445062754Glioblastoma TCGA",
  
      "publicationDatereleaseDate": null,
         "releaseNotesstatus":"this is a release note",
   "Available",
      "tissueTypeuri":null,          "platform":null,
  "/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQY8aIEDA",
      "processingFacilityversion":null,          "qcBy":null,
    "0.0.1"
    "qcDate":null
      }
   ],

  "totalNumberOfResults":2,    "paging":{

   }
}
11
}

Get a

...

Request

...

Dataset

This returns the primary fields of a dataset and links to get additional info.

Request

Code Block
curl -i -H Accept:application/json 'http://localhost:8080deflaux-test.appspot.com/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww/layer/agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww
agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQY8aIEDA'

Response

Code Block
HTTP/1.1 200 OK
ETag: 12404674072011502454
Content-Type: application/json
Transfer-EncodingDate: chunked
Server: Jetty(6.1.x)

{
   "name":"Flint HS Mice Affy",
Sun, 13 Feb 2011 00:27:44 GMT
Server: Google Frontend
Cache-Control: private, x-gzip-ok=""
Transfer-Encoding: chunked

{
  "annotations": "/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUwwagxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQY8aIEDA/layer/agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww/annotations",

  "idcreationDate":"agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww" 1297465568905,
  "creator": null,
  "description": null,
  "typeetag": "E2011502454",

  "versionhasClinicalData":"0.0.1",
 false,
  "descriptionhasExpressionData":"this false,
is a description"hasGeneticData": false,
  "id": "creationDateagxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQY8aIEDA":1296690778880,

  "urilayer": "/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUwwagxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQY8aIEDA/layer/agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww",
   "etagname": "1240467407Glioblastoma TCGA",
   "publicationDatereleaseDate": null,
   "releaseNotesstatus":"this is a release note "Available",

  "tissueTypeuri":null,    "platform":null,
   "processingFacility":null,
"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQY8aIEDA",
  "qcByversion":null,    "qcDate":null"0.0.1"
}

Get Annotations for a Dataset

This returns the annotations for a

...

dataset.

Request

Code Block
curl -i -H Accept:application/json 'http://localhost:8080deflaux-test.appspot.com/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww/layer/agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBwwagxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQY8aIEDA/annotations'

Response

Code Block
HTTP/1.1 200 OK
ETag: 923521-1609182934
Content-Type: application/json
Transfer-EncodingDate: chunkedSun, Server: Jetty(6.1.x)

{
   "id":"agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww",
   13 Feb 2011 00:27:44 GMT
Server: Google Frontend
Cache-Control: private, x-gzip-ok=""
Transfer-Encoding: chunked

{
  "creationDate": null,

  "uridateAnnotations":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww/layer/agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww/annotations" {},
  "doubleAnnotations": {},
   "etag": "923521-1609182934",

  "stringAnnotationsid":{ "agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQY8aIEDA",
  "longAnnotations": {},
   "floatAnnotationsstringAnnotations": {
    },"Disease": ["Cancer"],
    "dateAnnotationsInstitution":{ ["TCGA"],
    }"Number }

Create a layer

Request

Code Block

curl -i -H Accept:application/json -H Content-Type:application/json -d '{"name":"Flint HS Mice Affy", "type":"E", "description":"this is a description", "releaseNotes":"this is a release note"}' http://localhost:8080/of Samples": ["465"],
    "Reference / PubMed ID": ["18772890"],
    "Species": ["Human"],
    "Tumor / Tissue Type": ["Glioblastoma"]
  },
  "uri": "/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUwwagxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQY8aIEDA/layer

...

annotations"
}

Get all the Layers for a Dataset

This returns the primary fields for all the layers of a dataset.

Request

Code Block

HTTP/1.1 201 Created
ETag: 1240467407
Location: curl -i -H Accept:application/json 'http://deflaux-test.appspot.com/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUwwagxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQY8aIEDA/layer/agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww'

Response

Code Block

HTTP/1.1 200 OK
Content-Type: application/json
Transfer-EncodingDate: chunkedSun, Server: Jetty(6.1.x)

{
   "name":"Flint HS Mice Affy",
   "annotations":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww/layer/agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww/annotations",
   "id":"agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww",
   "type":"E",
   "version":"0.0.1",
   "description":"this is a description",
   "creationDate":1296690778880,
   "uri":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww/layer/agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww",
   "etag":"1240467407",
   "publicationDate":null,
   "releaseNotes":"this is a release note",
   "tissueType":null,
   "platform":null,
   "processingFacility":null,
   "qcBy":null,
   "qcDate":null
}

Now ask for the owning dataset and you can see the preview of the layer

Request

Code Block

curl -i -H Accept:application/json http://localhost:8080/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww

Response

Code Block

HTTP/1.1 200 OK
ETag: -801135512
Content-Type: application/json
Transfer-Encoding: chunked
Server: Jetty(6.1.x)

{
"name":"Flint HS Mice",
"annotations":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww/annotations",
"id":"agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww",
"version":"0.0.1",
"creator":"Jonathan Flint",
"description":null,
"creationDate":1296690549675,
"status":"Future",
"uri":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww",
"etag":"-801135512",
"releaseDate":null,
"layers":[
{
         "id":"agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww",
         "type":"E",
         "uri":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww/layer/agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww"
      },{
         "id":"use this uri to make a new layer",
         "type":"hack",
         "uri":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww/layer"
      }
]
}

Update a Layer

In the example below we updated the tissue type.

Request

Code Block

curl -i -H Accept:application/json -H Content-Type:application/json -X PUT -H ETag:1240467407 -d '
{
   "name":"Flint HS Mice Affy",
   "annotations":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww/layer/agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww/annotations",
   "id":"agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww",
   "type":"E",
   "version":"0.0.1",
   "description":"this is a description",
   "creationDate":1296690778880,
   "uri":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww/layer/agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww",
   "etag":"1240467407",
   "publicationDate":null,
   "releaseNotes":"this is a release note",
   "tissueType":"liver",
   "platform":null,
   "processingFacility":null,
   "qcBy":null,
   "qcDate":null
}' http://localhost:8080/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww/layer/agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww

Response

Code Block

HTTP/1.1 200 OK
ETag: 1424771925
Content-Type: application/json
Transfer-Encoding: chunked
Server: Jetty(6.1.x)

{
   "name":"Flint HS Mice Affy",
   "annotations":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww/layer/agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww/annotations",
   "id":"agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww",
   "type":"E",
   "version":"0.0.1",
   "description":"this is a description",
   "creationDate":1296690778880,
   "uri":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww/layer/agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww",
   "etag":"1424771925",
   "publicationDate":null,
   "releaseNotes":"this is a release note",
   "tissueType":"liver",
   "platform":null,
   "processingFacility":null,
   "qcBy":null,
   "qcDate":null
}

Delete a layer

Request

Code Block

curl -i -X DELETE http://localhost:8080/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww/layer/agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww

Response

Code Block

HTTP/1.1 204 No Content
Server: Jetty(6.1.x)

Add annotations to a layer

Request

Code Block

curl -i -H Accept:application/json -H Content-Type:application/json -X PUT -H ETag:923521 -d '
{
   "id":"agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww",
   "creationDate":null,
   "uri":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww/layer/agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww/annotations",
   "etag":"923521",
   "stringAnnotations":{
      "notes":["I threw away 6 samples during the curation process due to gender chromosome mismatches"]
   },
   "floatAnnotations":{

   },
   "dateAnnotations":{

   }
}' http://localhost:8080/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww/layer/agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww/annotations

Response

Code Block

HTTP/1.1 200 OK
ETag: -1897035229
Content-Type: application/json
Transfer-Encoding: chunked
Server: Jetty(6.1.x)

{
   "id":"agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww",
   "creationDate":null,
   "uri":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww/layer/agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww/annotations",
   "etag":"-1897035229",
   "stringAnnotations":{
      "notes":[
         "I threw away 6 samples during the curation process due to gender chromosome mismatches"
      ]
   },
   "floatAnnotations":{

   },
   "dateAnnotations":{

   }
}

Query API Usage Examples

Sort clause

Request

Code Block

curl -H Accept:application/json -i 'http://deflaux-test.appspot.com/repo/v1/query?query=select+*+from+dataset+order+by+"name"+limit+3+offset+1'

Response

Code Block

{
   "totalNumberOfResults":10,
   "results":[
      {
         "name":"Flint HS Mice",
         "id":"agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQY2q0DDA",
         "version":"0.0.1",
         "description":null,
         "status":"Future",
         "creator":"Jonathan Flint",
         "creationDate":1296182255070,
         "releaseDate":null,
         "hasExpressionData":true,
         "hasGeneticData":false,
         "hasClinicalData":false,
         "Disease":[
            "Normal Phenotypes"
         ],
         "Species":[
            "Mouse"
         ],
         "Number of Samples":[
            1027.0
         ]
      },
      {
         "name":"Glioblastoma TCGA",
         "id":"agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYseQDDA",
         "version":"0.0.1",
         "description":null,
         "status":"Available",
         "creator":null,
         "creationDate":1296182238229,
         "releaseDate":null,
         "hasExpressionData":true,
         "hasGeneticData":false,
         "hasClinicalData":false,
         "Disease":[
            "Cancer"
         ],
         "Tumor / Tissue Type":[
            "Glioblastoma"
         ],
         "Institution":[
            "TCGA"
         ],
         "Species":[
            "Human"
         ],
         "Reference / PubMed ID":[
            1.877289E7
         ],
         "Number of Samples":[
            465.0
         ]
      },
      {
         "name":"Harvard Brain Tissue Resource Center",
         "id":"agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYiZsEDA",
         "version":"0.0.1",
         "description":null,
         "status":"In Transition",
         "creator":"Francine Benes",
         "creationDate":1296182251551,
         "releaseDate":null,
         "hasExpressionData":true,
         "hasGeneticData":false,
         "hasClinicalData":false,
         "Disease":[
            "Neuro-degenerative"
         ],
         "Tumor / Tissue Type":[
            " Visual Cortex",
            "Prefrontal cortex",
            " Cerbellum"
         ],
         "Species":[
            "Human"
         ],
         "Institution":[
            "HBTRC"
         ],
         "Number of Samples":[
            700.0
         ]
      }
   ]
}

Where clause

Currently only '==' is supported on either primary fields or annotations

Request

Code Block

curl -H Accept:application/json -i 'http://deflaux-test.appspot.com/repo/v1/query?query=select+*+from+dataset+where+Species+==+"Human"'

Response

Code Block

{
   "totalNumberOfResults":10,
   "results":[
      {
         "name":"Pediatric AML TARGET",
         "id":"agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYgvcCDA",
         "version":"0.0.1",
         "description":null,
         "status":"In Transition",
         "creator":"Soheil Meshinchi",
         "creationDate":1296182253120,
         "releaseDate":null,
         "hasExpressionData":true,
         "hasGeneticData":false,
         "hasClinicalData":false,
         "Disease":[
            "Cancer"
         ],
         "Tumor / Tissue Type":[
            "AML (pediatric)"
         ],
         "Institution":[
            "FHCRC"
         ],
         "Species":[
            "Human"
         ],
         "Number of Samples":[
            200.0
         ]
      },
      {
         "name":"Glioblastoma TCGA",
         "id":"agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYseQDDA",
         "version":"0.0.1",
         "description":null,
         "status":"Available",
         "creator":null,
         "creationDate":1296182238229,
         "releaseDate":null,
         "hasExpressionData":true,
         "hasGeneticData":false,
         "hasClinicalData":false,
         "Disease":[
            "Cancer"
         ],
         "Tumor / Tissue Type":[
            "Glioblastoma"
         ],
         "Institution":[
            "TCGA"
         ],
         "Species":[
            "Human"
         ],
         "Reference / PubMed ID":[
            1.877289E7
         ],
         "Number of Samples13 Feb 2011 00:27:45 GMT
Server: Google Frontend
Cache-Control: private, x-gzip-ok=""
Transfer-Encoding: chunked

{
  "paging": {},
  "results": [],
  "totalNumberOfResults": 0
}

Get a Dataset Layer

This returns the primary fields of the dataset layer and links to get additional info.

TODO add an example here

Get Annotations for a Dataset Layer

This returns the annotations for a dataset layer.

TODO add an example here

REST API Usage Examples (Read/Write and slightly out of date)

This is a REST api (see Service API Design for more details as to what this means). You can create entities, updated entities, read entities, and delete entities. More advanced querying will be implemented as a separate API. Partial updates (e.g., just updating two fields in a dataset) are not supported. In a nutshell, when you update something like a dataset, you GET the dataset first, modify the properties you want to change, and then send the entire object back to the service so that this revised entity overwrites the previously stored entity.

Create a Dataset

Request:

Code Block

curl -i -H Accept:application/json -H Content-Type:application/json
-d '{"name":"test dataset", "creator":"fake creator", "releaseDate":"2009-10-01", "status":"not curated"}'
http://localhost:8080/repo/v1/dataset

Response

Code Block

HTTP/1.1 201 Created
ETag: 1736839268
Location: /repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYBAw
Content-Type: application/json
Transfer-Encoding: chunked
Server: Jetty(6.1.x)

{
   "name":"test dataset",
   "annotations":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYAQw/annotations",
   "id":"agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYAQw",
   "version":"0.0.1",
   "creator":"fake creator",
   "description":null,
   "creationDate":1296595870715,
   "status":"not curated",
   "uri":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYAQw",
   "etag":"1309185941",
   "releaseDate":1254355200000,
   "layers":[]
}

Update a Dataset

Note that in the example below the creator and description fields have been changed but all others remain the same.

Request:

Code Block

curl -i -H Accept:application/json -H Content-Type:application/json -X PUT -H ETag:1309185941 -d '{
   "name":"test dataset",
   "annotations":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYAQw/annotations",
   "id":"agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYAQw",
   "version":"0.0.1",
   "creator":"updated creator",
   "description":"I just added a description",
   "creationDate":1296595870715,
   "status":"not curated",
   "uri":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYAQw",
   "etag":"1309185941",
   "releaseDate":1254355200000,
   "layers":[]
}
' http://localhost:8080/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYAQw

Response

Code Block

HTTP/1.1 200 OK
ETag: -852418664
Content-Type: application/json
Transfer-Encoding: chunked
Server: Jetty(6.1.x)

{
   "name":"test dataset",
   "annotations":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYAQw/annotations",
   "id":"agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYAQw",
   "version":"0.0.1",
   "creator":"updated creator",
   "description":"I just added a description",
   "creationDate":1296595870715,
   "status":"not curated",
   "uri":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYAQw",
   "etag":"-852418664",
   "releaseDate":1254355200000,
   "layers":[]
}

Add Annotations to a Dataset

First get the empty annotations container for your newly created dataset

Request

Code Block

curl -i -H Accept:application/json http://localhost:8080/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYAQw/annotations

Response

Code Block

HTTP/1.1 200 OK
ETag: 923521
Content-Type: application/json
Transfer-Encoding: chunked
Server: Jetty(6.1.x)

{
   "id":"agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYAQw",
   "creationDate":null,
   "uri":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYAQw/annotations",
   "etag":"923521",
   "stringAnnotations":{

   },
   "floatAnnotations":{

   },
   "dateAnnotations":{

   }
}

Then you add/modify the annotations of interest and do a PUT. Note that annotation values must always be list values even if the list is only of length one.

Request

Code Block

curl -i -H Accept:application/json -H Content-Type:application/json -X PUT -H ETag:923521 -d '{
   "id":"agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYAQw",
   "creationDate":null,
   "uri":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYAQw/annotations",
   "etag":"923521",
   "stringAnnotations":{
        "Experimental Design Templates":["exp-122887", "exp-97765"]
   },
   "floatAnnotations":{
        "Number of Samples":[500]
   },
   "dateAnnotations":{
        "Publication Date":["2011-01-15"]
   }
}' http://localhost:8080/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYAQw/annotations

Response

Code Block

HTTP/1.1 200 OK
ETag: -1638393853
Content-Type: application/json
Transfer-Encoding: chunked
Server: Jetty(6.1.x)

{
   "id":"agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYBww",
   "creationDate":null,
   "uri":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYBww/annotations",
   "etag":"-1638393853",
   "stringAnnotations":{
      "Experimental Design Templates":[
         "exp-122887",
  465.0       "exp-97765"
   ]   ]
   },
   "floatAnnotations":{
  {    "Number of Samples":[
   "name":"TCGA Curation Package",     500.0
    "id":"agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYgfQDDA",  ]
   },
   "versiondateAnnotations":"0.0.1",{
      "Publication   Date"description":null,[
         "status":"Available",1295049600000
      ]
  "creator":null,
         "creationDate":1296182242619,
         "releaseDate":null,
         "hasExpressionData":true,
         "hasGeneticData":false, }
}

Delete a Dataset

Request

Code Block

curl -i -X DELETE http://localhost:8080/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYAQw

Response

Code Block

HTTP/1.1 204 No Content
Server: Jetty(6.1.x)

Get a Layers for a Dataset

Request

Code Block

curl -i -H Accept:application/json http://localhost:8080/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww/layer

Response

Code Block

HTTP/1.1 200 OK
Content-Type: application/json
Transfer-Encoding: chunked
Server: Jetty(6.1.x)

{
   "results":[
      {
  "hasClinicalData":false,          "Diseasename":["Flint HS            "Cancer"
         ]Mice Affy",
         "Tumor / Tissue Type":[
annotations":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww/layer/agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww/annotations",
           "Multiple""id":"agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww",
         ]"type":"E",
         "Institutionversion":["0.0.1",
         "description":"this is a description"TCGA",
         ]"creationDate":1296690778880,
         "Speciesuri":["/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww/layer/agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww",
            "Human""etag":"1424771925",
         ]"publicationDate":null,
         "Number of SamplesreleaseNotes":["this is a release note",
        2400.0
  "tissueType":"liver",
       ]  "platform":null,
    },     "processingFacility":null,
 {          "nameqcBy":"Hepatocellular Carcinoma HongKong"null,
         "idqcDate":"agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQY0YMEDA",null
      },
    "version":"0.0.1",  {
         "descriptionname":null"Flint HS Mice Phenotypes",
         "statusannotations":"Available/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww/layer/agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjpBww/annotations",
         "creatorid":"John LukagxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjpBww",
         "creationDatetype":1296182245850"C",
         "releaseDateversion":null"0.0.1",
         "hasExpressionDatadescription":true"this is a description",
         "hasGeneticDatacreationDate":false1296693007167,
         "hasClinicalDatauri":false"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww/layer/agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjpBww",
         "Diseaseetag":["1445062754",
         "publicationDate":null,
  "Cancer"       "releaseNotes":"this is a ]release note",
         "Tumor / Tissue TypetissueType":[null,
            "HCCplatform":null,
         ]"processingFacility":null,
         "SpeciesqcBy":[
  null,
         "HumanqcDate":null
      }
   ],
     
   "InstitutiontotalNumberOfResults":[2,
   "paging":{

   }
}

Get a Layer

Request

Code Block
curl "HKU"
         ],
     -i -H Accept:application/json http://localhost:8080/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww/layer/agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww

Response

Code Block

HTTP/1.1 200 OK
ETag: 1240467407
Content-Type: application/json
Transfer-Encoding: chunked
Server: Jetty(6.1.x)

{
   "Number of Samplesname":[
      "Flint HS Mice Affy",
   "annotations":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww/layer/agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww/annotations",
 250.0  "id":"agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww",
   "type":"E",
   ]"version":"0.0.1",
   "description":"this is a }description",
   "creationDate":1296690778880,
  {
   "uri":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww/layer/agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww",
      "nameetag":"Human Liver Cohort1240467407",
     "publicationDate":null,
   "idreleaseNotes":"agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYuYsEDAthis is a release note",
     "tissueType":null,
   "versionplatform":"0.0.1"null,
   "processingFacility":null,
     "descriptionqcBy":null,
   "qcDate":null
}

Get annotations for a layer

Request

Code Block
curl -i -H  "status":"Available",
         "creator":"Guengrich, Strom, Schuetz",
         "creationDate":1296182248134,
     Accept:application/json http://localhost:8080/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww/layer/agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww/annotations

Response

Code Block

HTTP/1.1 200 OK
ETag: 923521
Content-Type: application/json
Transfer-Encoding: chunked
Server: Jetty(6.1.x)

{
   "id":"agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww",
   "releaseDatecreationDate":null,

        "hasExpressionDatauri":true,
         "hasGeneticData":false,
     "/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww/layer/agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww/annotations",
   "hasClinicalDataetag":false,
  "923521",
      "DiseasestringAnnotations":[{

   },
       "Cardiovascular Disease""floatAnnotations":{

   },
   "dateAnnotations":{
],
   }
}

Create a layer

Request

Code Block
curl -i  "Tumor / Tissue Type":[
            "Liver"
         ],
         "Species":[
            "Human"
         ],
         "Institution":[
            " Pittsburg",
            " St. Judes",
            "Vanderbilt"
         ],
         "Reference / PubMed ID":[
            1.8462016E7
         ],
         "Number of Samples":[
            517.0
         ]
      },
      {
         "name":"METABRIC Breast Cancer",
         "id":"agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYoZMEDA",
         -H Accept:application/json -H Content-Type:application/json -d '{"name":"Flint HS Mice Affy", "type":"E", "description":"this is a description", "releaseNotes":"this is a release note"}' http://localhost:8080/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww/layer

Response

Code Block

HTTP/1.1 201 Created
ETag: 1240467407
Location: /repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww/layer/agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww
Content-Type: application/json
Transfer-Encoding: chunked
Server: Jetty(6.1.x)

{
   "name":"Flint HS Mice Affy",
   "annotations":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww/layer/agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww/annotations",
   "id":"agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww",
   "type":"E",
   "version":"0.0.1",
   "description":"this is a description",
   "creationDate":1296690778880,
   "uri":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww/layer/agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww",
   "etag":"1240467407",
   "publicationDate":null,
   "releaseNotes":"this is a release note",
   "tissueType":null,
   "platform":null,
   "processingFacility":null,
   "qcBy":null,
   "qcDate":null
}

Now ask for the owning dataset and you can see the preview of the layer

Request

Code Block

curl -i -H Accept:application/json http://localhost:8080/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww

Response

Code Block

HTTP/1.1 200 OK
ETag: -801135512
Content-Type: application/json
Transfer-Encoding: chunked
Server: Jetty(6.1.x)

{
"name":"Flint HS Mice",
"annotations":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww/annotations",
"id":"agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww",
"version":"0.0.1",
         "creator":"Jonathan Flint",
"description":null,
         "creationDate":1296690549675,
"status":"Future"In Transition,
"uri":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww",
         "creator"etag":"Aparicio-801135512",
Caldas"releaseDate":null,
"layers":[
{
         "creationDateid":1296182250209"agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww",
         "releaseDatetype":null"E",
         "hasExpressionData":true,uri":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww/layer/agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww"
      },{
         "hasGeneticDataid":false,"use this uri to make a new    "hasClinicalData":falselayer",
         "Diseasetype":["hack",
            "Cancer"uri":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww/layer"
      }
  ],
         "Tumor / Tissue Type":[
            "Breast"
         ],
         "Institution":[
            "BCCA Cambridge"
         ],
         "Species":[
            "Human"
         ],
         "Number of Samples":[
            1500.0
         ]
      },
      {
         "name":"Harvard Brain Tissue Resource Center",
         "id":"agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYiZsEDA",
     }

Update a Layer

In the example below we updated the tissue type.

Request

Code Block

curl -i -H Accept:application/json -H Content-Type:application/json -X PUT -H ETag:1240467407 -d '
{
   "name":"Flint HS Mice Affy",
   "annotations":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww/layer/agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww/annotations",
   "id":"agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww",
   "type":"E",
   "version":"0.0.1",
   "description":"this is a description",
   "creationDate":1296690778880,
   "uri":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww/layer/agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww",
   "etag":"1240467407",
   "publicationDate":null,
   "releaseNotes":"this is a release note",
   "tissueType":"liver",
   "platform":null,
   "processingFacility":null,
   "qcBy":null,
   "qcDate":null
}' http://localhost:8080/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww/layer/agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww

Response

Code Block

HTTP/1.1 200 OK
ETag: 1424771925
Content-Type: application/json
Transfer-Encoding: chunked
Server: Jetty(6.1.x)

{
   "name":"Flint HS Mice Affy",
   "annotations":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww/layer/agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww/annotations",
   "id":"agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww",
   "type":"E",
   "version":"0.0.1",
   "description":"this is a description",
   "descriptioncreationDate":null1296690778880,
    "uri":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww/layer/agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww",
    "statusetag":"In Transition1424771925",
     "publicationDate":null,
   "creatorreleaseNotes":"Francinethis Benes",is a     release note",
   "creationDatetissueType":1296182251551,
     "liver",
   "releaseDateplatform":null,
     
   "hasExpressionDataprocessingFacility":truenull,
         "hasGeneticData"qcBy":false,
     null,
   "hasClinicalDataqcDate":false,null
}

Delete a layer

Request

Code Block
curl -i -X DELETE http://localhost:8080/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww/layer/agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww

Response

Code Block
 "Disease":[
            "Neuro-degenerative"
         ],
         "Tumor / Tissue Type":[
   HTTP/1.1 204 No Content
Server: Jetty(6.1.x)

Add annotations to a layer

Request

Code Block

curl -i -H Accept:application/json -H Content-Type:application/json -X PUT -H ETag:923521 -d '
{
   "id":"agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww",
   "creationDate":null,
   "uri":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww/layer/agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww/annotations",
   "etag":"923521",
   "stringAnnotations":{
        " Visual Cortex",
            "Prefrontal cortex",
    "notes":["I threw away 6 samples during the curation process due to gender chromosome mismatches"]
   },
   " CerbellumfloatAnnotations":{

   },
   "dateAnnotations":{
],
   }
     "Species":[
            "Human"
         ],
         "Institution":[
   }' http://localhost:8080/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww/layer/agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww/annotations

Response

Code Block

HTTP/1.1 200 OK
ETag: -1897035229
Content-Type: application/json
Transfer-Encoding: chunked
Server: Jetty(6.1.x)

{
   "id":"agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww",
   "creationDate":null,
   "uri":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww/layer/agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww/annotations",
   "etag":"-1897035229",
   "stringAnnotations":{
        "HBTRCnotes":[
         ],"I threw away 6 samples during the curation process due "Number of Samples":[to gender chromosome mismatches"
      ]
   },
 700.0  "floatAnnotations":{

   },
  ] "dateAnnotations":{

    }
   ]
}