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The image below shows the variables tab for the simulated dataset CNSIM used within the v4 Tutorial for DataSHIELD users.
The table below summarises the column names in the variables tab, including examples from the test data built into the training environment in the spreadsheet image above.
Column Names | Description | Default value | Example value in the test data | Notes | ||
|---|---|---|---|---|---|---|
table | the table name the variable will be added to | Table | Column A (CNSIM) | This is the table name you refer to in your DataSHIELD login details.
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name | the variable name | Column B (e.g. LAB_TSC) | Mandatory field. | |||
valueType | the value type of the variable | text | Column C (e.g. decimal, integer) | |||
entityType | Opal can store data on different entities | Participant | Column D (e.g. Participant) | Examples: Participant (each row corresponds to a different participant), Instrument, Area, Drug | ||
referencedEntityType | if the variable values are entity identifiers, this is the type of the entities that are referenced | Column E | Can be left blank | |||
mimeType | the mime type of the variable to help applications to display documents | Column F | Examples: image/jpeg, application/excel. Can be left blank | |||
unit | the unit in which variables are expressed | Column G (e.g. Participant) | Examples: cm, kg, ml etc. Can be left blank | |||
repeatable | repeatable measurements | 0 | Column H (0) | 1 if repeatable, 0 if not (e.g. Three measures of blood pressure) | ||
occurrenceGroup | name of a repeatable variable group | Column I | Example: [ | |||
label:en | label of the variable. | Column J | Can be localized by language e.g. label:en in english, label:fr for french) | |||
| alias | Alternative name for the variable, usually used for defining a shorter name for the variable | Column K |
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The image below shows the categories tab for the simulated dataset CNSIM used within the v4 Tutorial for DataSHIELD users. Each category for each variable is represented by a single row in the spreadsheet. For example, in the dictionary file below, 3 rows (rows 12-14 inclusive) are for PM_BMI_CATEGORICAL as it has 3 categories.
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Column Names | Description | Default value | Example value in the test data | Notes | ||
|---|---|---|---|---|---|---|
table | the table name the variable will be added to | Table | Column A (CNSIM) | This is the table name you refer to in your DataSHIELD login details.
| ||
variable | the variable name (mandatory field) | Column B (e.g. DIS_CVA) | mandatory field. One row per category for each variable. | |||
name | the variable category | integer | Column C (e.g. 1) | mandatory field. One row per category for each variable | ||
code | can be left blank | Column D | Can be left blank | |||
missing | Some categories are interpreted as missing answers (e.g. 'Don't know', 'Prefer not to answer'). | 0 | Column E | Use 1 for missing and 0 for not missing (normal answer). | ||
label:en | label of the variable category | Column F | Human readable text description of the category. Can be localized by language e.g. label:en in english, label:fr for french) |
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- To create a new project click on the
Projecttab in the top left (after clicking it appears in green on the dark blue horizontal bar) - click
Add Project.
| Section |
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Fill in the details of your project:
- You must specify a name and this will be used to point to the data. For convenience do not use a very long name. The example below shows the name as CNSIM.
- The "title" can then be a longer explanatory label for the table
- The database currently defaults to mongodb but can also be MySQL
- You can give an additional description if you wish
| Info | ||
|---|---|---|
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In DataSHIELD in order to refer uniquely to a table held in Opal you must specify both the Opal |
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To upload data files from your local computer, click on
Dashboardfrom the top menu bar (the word changes to green)- Click
Manage Filesfrom the left hand menu
| Section |
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- By default, you will see a list of files currently held in your
Opal Home folder. This is where your dictionary and data files will be saved.
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- Click the grey
Uploadbutton from the top tab
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- This brings up a new window, click
Choose file
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- Browse to the .xls file to upload from your your local machine
- Select that file and click
open(you can simply double-click the file in Windows) - Clicking the dark blue
uploadat the bottom of the window - If that file already exists in that location then it will ask you whether to replace it or not (see above tip)
- Repeat for the .csv (data file)
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- Click on the
Projectstab from the top menu (it will turn green) and click on your project name (CNSIMin the example below) - Click on the large blue
+Add Tablebutton that sits above the list of tables in the project you have specified - Select
Add/update tables from dictionary ...from the drop down menu
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- Locate the data dictionary (.xls) file you have uploaded by clicking
Browse.
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- Use
HOMESandSYSTEMon your left menu to navigate to the folder that holds the .xls data dictionary file - Click the small square box to the left of the file name (a tick appears) and then click the dark blue
Selectbutton towards the bottom right
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- Click the blue
Nextbutton - Review the Opal table in the pop up window. If this is a new data table the information in the window should tell you the name of the Table you have asked to be created and the number of New Variables (corresponding to number of columns in your .csv data file).
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- If the information is correct, click the small box to the left of the table name (CNSIM in the example below). A tick will appear.
- Click the dark blue
Finishbutton from the bottom right
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- This will take you back to the list of all available tables in the chosen project, and after a few seconds this will be refreshed to include the new table you have create
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- Select your project again by clicking on the
Projectstab from the top menu and click on your project name (CNSIMin this particular example) - Your table states as holding 0
Entities(indicating it is empty)
| Section |
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- Click on the small box at the left of the table name, and a tick will appear.
- Click the grey
Importbutton from the tabs above the table. This opens a window to define file format.
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| Tip |
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Your data has now successfully been uploaded into an Opal server. You will need to repeat the process for each Opal server you wish to use. To start using the DataSHIELD training environment sit our Tutorial for DataSHIELD users using your own data. The tutorial teaches you the basics of DataSHIELD including how to:
Assistance with DataSHIELD can be found:
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Opal is supported by the software creators at Obiba. Opal support is available on the Obiba-users mailing list, where support questions can be posted for free. Opal general enquiries can be sent to info@obiba.org.