How to curate a sample in BioSamples

User requirements

I want to improve the quality of metadata for a sample in BioSamples, but I am not the owner of the sample.

Requirements

You need a Webin submission account to proceed with this recipe. Please refer to our Authentication Guide for more information.

Steps

Get the JSON Web Token from the Webin Authentication Service

Start by obtaining your Webin authentication JWT to use in your application. Please refer to our Authentication Guide for details.
Produce a BioSamples curation object in JSON format

To update a field in a sample if you are not the sample owner, create a BioSamples curation object. Populate the attributesPre field with the current value and the attributesPost field with the new value. See Submit curation object for an example POST request.

Example sample (simplified):

"name": "OAR_USU_Benz2616_LNG",
"accession": "SAMN08432304",
"domain": "self.BiosampleImportNCBI",
"release": "2018-01-29T00:00:00Z",
"update": "2018-06-08T16:22:08.220Z",
"characteristics": {
  "breed": [
    {
      "text": "Rambouillet"
    }
  ],
  "development stage": [
    {
      "text": "adult"
    }
  ]
}

Suppose we want to add an ontology code to the development stage attribute:

Before:

{
  "type": "development stage",
  "value": "adult"
}

After:

{
  "type": "development stage",
  "value": "adult",
  "iri": [
    "http://www.ebi.ac.uk/efo/EFO_0001272"
  ]
}

To apply this curation to sample SAMN08432304, create a curation object like:

{
  "sample": "SAMN08432304",
  "curation": {
    "attributesPre": [
      {
        "type": "development stage",
        "value": "adult"
      }
    ],
    "attributesPost": [
      {
        "type": "development stage",
        "value": "adult",
        "iri": [
          "http://www.ebi.ac.uk/efo/EFO_0001272"
        ]
      }
    ],
    "externalReferencesPre": [],
    "externalReferencesPost": []
  }
}

Submit the curation object to BioSamples using a POST request

You can now submit the curation object using your preferred HTTP client. Here’s how to do it with curl:

curl 'https://www.ebi.ac.uk/biosamples/samples/SAMN08432304/curationlinks' \
     -i -X POST \
     -H 'Content-Type: application/json' \
     -H 'Authorization: Bearer $TOKEN' \
     -d '{
       "sample": "SAMN08432304",
       "curation": {
         "attributesPre": [
           {
             "type": "development stage",
             "value": "adult"
           }
         ],
         "attributesPost": [
           {
             "type": "development stage",
             "value": "adult",
             "iri": [
               "http://www.ebi.ac.uk/efo/EFO_0001272"
             ]
           }
         ],
         "externalReferencesPre": [],
         "externalReferencesPost": []
       }
     }'

Templates

Attribute and external reference curation template

{
  "sample": "<accession-of-the-interest-sample>",
  "curation": {
    "attributesPre": [
      {
        "type": "<attribute-name>",
        "value": "<attribute-value>",
        "iri": ["<existing-iri-if-any>"]
      }
    ],
    "attributesPost": [
      {
        "type": "<new-attribute-name>",
        "value": "<new-attribute-value>",
        "iri": ["<new-iri-if-any>"]
      }
    ],
    "externalReferencesPre": [
      {
        "url": "<URL-of-external-reference-to-replace>"
      }
    ],