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Info

Opal servers require that a formal data dictionary is specified and uploaded in order that a data set can be properly imported.

Opal accepts various various formats but in this tutorial a .csv is used for the data file and Microsoft Excel for the data dictionary file (.xls or .xlsx).  

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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.

Note
It is critical that the table name appears in every row


name

the variable name


Column B (e.g. LAB_TSC)

Mandatory field.
Becomes the the column name in Opal for that variable

valueType

the value type of the variable

text

Column C (e.g. decimal, integer)

See further information on variable types and classes

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: [measure value, measure date] is a group of variables that can be repeated. Can be left blank

label:en

label of the variable.


Column J

Can be localized by language e.g. label:en in english, label:fr for french)

aliasAlternative name for the variable, usually used for defining a shorter name for the variable
Column K

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  • Click on the Projects tab from the top menu (it will turn green) and click on your project name (CNSIM in the example below)
  • Click on the large blue +Add Table button that sits  above the list of tables in the project you have specified
  • Select Add/update tables from dictionary ... from the drop down menu
Section

Section

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Tip

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:

  • login
  • run commands to:
    • generate descriptive statistics
    • subset tables and vectors
    • fit some regression models

Assistance with DataSHIELD can be found:

Delete tables from Opal

It is simple to delete a file once it has been uploaded to Opal, you can practice by selecting the alspacsim.csv file (or your own data file) you have just uploaded. 

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  • Click on the Projects tab from the top menu (it will turn green) and click on your project name (CNSIM in the example below)
  • Tick the data table you wish to archive e.g. CNSIM3 in the example below and click the Export button (top right)
Section


  • You can choose to export as a .csv file or as a compressed Opal archive file.


Tip
titleOpal archive files

The .csv is just the data file. The Opal archive file is a .zip file containing the data file (.csv) and the data dictionary for that file all ready formatted to be imported into Opal.

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