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Data entry/data upload

 

During this step the data are collected in the OpenClinica database. Data can be entered manually in OpenClinica via the user interface. There is no need for retyping in OpenClinica if the data are already available in an electronic format. In this case the dataset can be uploaded in OpenClinica via the ‘Import Data’ function.

For all types of data entry you need to have a user account in OpenClinica. If you have not built the study/CRFs yourself or if you do not have a user account, see step  Request study on OpenClinica.nl in the preparation phase. The user account needs to be requested by a person who has the role of data manager or study director in the OpenClinica study.  For more information about user types and roles within OpenClinica, see: https://docs.openclinica.com/3.1/openclinica-user-guide/overview-user-types-and-roles/actionsbuttons-allowed-user-role

It is recommended to let the OpenClinica study role correspond to the tasks delegated by the Principal Investigator on the Delegated Task List  to ensure that members of the research staff to whom specific study tasks have been delegated (by the principal investigator) are qualified to perform those tasks as demonstrated by evidence of their education, training and experience.

 

Manual data entry in OpenClinica
It is possible to enter data manually in OpenClinica via the user interface. Please see the data entry manual for explanation.

 

Upload of existing data

It is possible to upload existing data in OpenClinica via the Import Data module. For this, you first need to convert your data file into the ODM XML format, which is the only format that OpenClinica supports. Transformation of the data into this format can be done with the OpenClinica Data Importer tool.

The tool also performs  data checks (verifies if the data definitions in the dataset correspond to the CRF definitions in OpenClinica). If the definitions do not match, you will receive clear messages indicating what needs to be changed (either data in the dataset or CRF definitions in OpenClinica). The Import Data module in OpenClinica only allows to import data, not to create subjects or to schedule events. If your dataset contains data for new subjects or for events that have not been scheduled, a specific file will be created by the data importer tool.

The OpenClinica system administrators can create the subjects or schedule the events in your OpenClinica study using this file. You can contact the TraIT Servicedesk (servicedesk@ctmm-trait.nl) to request this.

The upload of data in OpenClinica always needs to be tested before it can be performed on the production server. There is a specific ‘upload test server’ available for testing.

If upload succeeds on ‘upload test server’, a final rehearsal of the data upload needs to be performed on the OpenClinica acceptance server. This is an exact copy of the production server. If this succeeds, you can perform the actual upload on the production server. The OpenClinica Data Importer tool and a user manual are available in the knowledge base section of the TraIT Servicedesk.

Note: uploading data in OpenClinica is a complex process. OpenClinica users that have experience with building studies and CRFs and have some programming knowledge should be able to complete the process successfully (type advanced data manager).

The process is still in development and any feedback is welcome.

Please find below the steps that you need to follow to upload data in the production server:

Step 0: Preparation

  1. Download the OpenClinica Data Importer and user manual from the TraIT Servicedesk knowledge base.
    There are two versions available: the MSI file can be used if you have administrator rights on your computer; it contains both the importer tool and the manual. If you do not have administrator rights on your computer, you will need to download the OCDataImporter exe file and separately download the manual.

Step 1: Prepare Test Server

  1. Request a study and user account on the TraIT upload test server. For this, please create a ticket in TraIT Servicedesk and use the data upload request form that can be downloaded from the TraIT Servicedesk knowledge base (Task 1 one the form).
  2. Build your study and CRFs on the upload test server identically as (will be) done on the production server (no need to build/upload the rules; rules are not ran during upload).
  3. Download the study metadata. This file contains server specific information required for the upload.

Step 2: Create Subjects and Events

  1. Run the data importer tool on the dataset that you want to upload.  The advice is to create one data set per Event (may be more CRFs)

a. Correct mistakes (regarding Subjects, Events) by adjusting the data in the source file (in that case you will need to run the tool again)

b. Request inserts of the Subjects and Events with the data upload request form (Task 2 on the form). Attach the *.sql insert files to the Topdesk ticket.

2. Verify subject attribute data and event data via the OpenClinica user interface

NB: this process needs to be repeated for each Event (event needs to be selected when running OCDataImporter). The sql files will be overwritten, so make sure that you move the *.sql insert files to a separate folder before running the DataImporter for another Event.

Please request the inserts in batch; for all Subjects and Events at one time

Step 3: Upload data

  1. Run the data importer tool on the dataset that you want to upload
  • Correct mistakes in CRF data by updating the CRF or adjusting the data in the source file (in that case you will need to run the tool again).

2. Upload the ODM XML  files that were produced by the data importer tool via the OpenClinica Import Data module

3.Verify uploaded data via the OpenClinica user interface

NB: please be aware that the *.ODM will be overwritten, so make sure that you move the *.ODM files to a separate folder before running the DataImporter for another Event.

If steps 2 and 3 were completed successfully, store your final ODM datafile(s) and sql insert files.

Step 4: Prepare openclinica.nl server

  1. If the study does not  yet exist on the OpenClinica production server
  • Request a new study (and possibly also a user account) on the production server. You can request this using the TraIT Servicedesk web form for a new study.
  • Build the study exactly as done on the upload test server.
  • If the study does exist, make sure that the study on the production server matches the study on the upload test server
  • Step 5: Prepare acceptance server

    NB: the acceptance server is a copy of the production server; all OpenClinica.nl studies and users are present on this server.

    1. Request access on the OpenClinica acceptance server and indicate that you want to rehearse the data upload. Please do this via the data upload request form (Task 3).
    • Remark: the person who performs the upload in the OpenClinica study should have a user account on the OpenClinica production server and role data manager or study director in the study.
  • Download the study metadata
  • a) If -part of the- Subjects or Events are not yet present/scheduled on the production server, these can be created via inserts in the database. For this you need to repeat step 2: Create Subjects and Events using the newly downloaded study metadata and your final insert file(s).
    Use the data upload request form to request this (Task 4a).
    b) If -part of the- Subjects already exist on the production server then the Subject IDs in the dataset need to be replaced by the OpenClinica Study Subject oid’s. Use the data upload request form to request a table with the OpenClinica Study Subject oid’s (Task 4b in the form). The OpenClinica DataImporter needs to be ran on this table in order to replace the Study Subject ID’s in the data file.
  • Repeat Step 3: Uploading data using the newly downloaded study metadata and your final ODM data file(s).

    If Step 5 was completed successfully, store your final insert files and your ODM XML file(s).

    Step 6: Upload data on production server: openclinica.nl

    1. If -part of the- Subjects or Events are not yet present/scheduled on the production server, request insert of the final insert files via the TraIT Servicedesk (the same insert files as used in step 5, nr 3a). Please use the data upload request form for this (Task 5)
      If -part of the- the subjects already exist on the production server, then you can use the ODM file that you received from the TraIT servicedesk (step 5, nr 3b).
    2. Upload the final ODM file(s) via the OpenClinica Import Data module

     

    Next step: Manage Study

    Back to: Execution Phase