Submissions

Operations related to submitting or modifying data in BioStudies database.

Submission

POST http://biostudy-prod.ebi.ac.uk:8788/submissions

Perform a submission to BioStudies using the given page tab. Please be aware of the following: - The given page tab should match the format specified in the SUBMISSION_TYPE header - Regardless of the chosen format to submit, the page tab document in the response will always be returned in JSON format - Any referenced file should be either placed in the user folder or attached to the request using the Files parameter. Please have in mind that the amount of files that can be directly attached to the request is limited, if the submission has too many files, please place them in the user directory. - If no accession number is provided, a new submission will be created and the corresponding accession number will be generated - If an accession number is provided, the submission will be treated as a resubmission which will perform an update Example For JSON submission: curl -X POST \ -H "X-SESSION-TOKEN: <authToken>" \ -H "Submission_Type: application/json" \ -F 'Submission={ "type": "Submission", "accno": "S-BIAD1", "section": { "type": "Study" } }'

Query Parameters

Name	Type	Description
onBehalf	string	In case the submission is performed on behalf of another user, the submission owner's email should be placed in this parameter.
sse	boolean	In case the submission is performed on behalf of another user, this parameter indicates whether a new user should be registered in case the given owner doesn't exist.
name	string	Name that will be used to create the new user in case the "sse" parameter is set to true.

Headers

Name	Type	Description
X-SESSION-TOKEN	string	User authentication token
Submission_Type	string	Page tab format used to perform the submission. Accepted values based on the format are: - JSON: application/json - TSV: text/plain - XML: text/xml

Request Body

Name	Type	Description
	string	Submission page tab in the chosen format
Submission	string	List of files to be attached to the submission
fileMode	string	Indicates whether the files in the submission should be copied or moved from the user folder. The files will be copied by default. Accepted values: COPY MOVE
Attributes	string	List of attributes that allow overriding any value at the submission level in the submitted page tab. The values should be passed in the key=value format i.e. title=new title

200

{
  "type": "Submission",
  "accno": "S-BIAD1",
  "section": {
    "type": "Study"
  }
}

401

Full authentication is required for this endpoint

Direct Submission

POST http://biostudy-prod.ebi.ac.uk:8788/submissions/direct

Perform a submission to BioStudies using the page tab inside the given file. Please be aware of the following: - The given page tab should match the format specified in the SUBMISSION_TYPE header - Regardless of the chosen format to submit, the page tab document in the response will always be returned in JSON format - Any referenced file should be either placed in the user folder or attached to the request using the Files parameter. Please have in mind that the amount of files that can be directly attached to the request is limited, if the submission has too many files, please place them in the user directory. - If no accession number is provided, a new submission will be created and the corresponding accession number will be generated - If an accession number is provided, the submission will be treated as a resubmission which will perform an update Example For JSON submission: curl -X POST \ -H "X-SESSION-TOKEN: <authToken>" \ -H "Submission_Type: text/plain" \ -F 'Submission=submission.tsv}'

Query Parameters

Name	Type	Description
onBehalf	string	In case the submission is performed on behalf of another user, the submission owner's email should be placed in this parameter.
sse	boolean	In case the submission is performed on behalf of another user, this parameter indicates whether a new user should be registered in case the given owner doesn't exist.
name	string	Name that will be used to create the new user in case the "sse" parameter is set to true.

Headers

Name	Type	Description
X-SESSION-TOKEN	string	User authentication token
Submission_Type	string	Page tab format used to perform the submission. Accepted values based on the format are: - JSON: application/json - TSV: text/plain - XML: text/xml

Request Body

Name	Type	Description
Submission	string	Submission page tab in the chosen format
Files	string	List of files to be attached to the submission
fileMode	string	Indicates whether the files in the submission should be copied or moved from the user folder. The files will be copied by default. Accepted values: COPY MOVE
Attributes	string	List of attributes that allow overriding any value at the submission level in the submitted page tab. The values should be passed in the key=value format i.e. title=new title

200

{
  "type": "Submission",
  "accno": "S-BIAD1",
  "section": {
    "type": "Study"
  }
}

401

Full authetication is required for this endpoint

Submission

DELETE http://biostudy-prod.ebi.ac.uk:8788/submissions/{accNo}

Deletes the submission with the given accession number

Path Parameters

Name	Type	Description
accNo	string	Submission accession number

Headers

Name	Type	Description
X-SESSION-TOKEN	string	User authentication token

200