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Introduction

This user manual will guide you through the process of uploading data to the DataHub infrastructure via the drop zones method. 

Before you start!

Prerequisites and general conditions for uploading new data are: 

  • You have been assigned a project from the DataHub intake interview. If not, please refer to this page: Starting a new project
  • You are connected to the UM- or MUMC-network. Either physically or via VPN.
  • You are using a recent version of a compatible web browser
  • You have an UM- or MUMC-account
  • You have the drop zones network drive mounted:
    • (Windows users) The network drive W:\ should be visible from Windows Explorer - My Computer.
      In case you don't see the W:\ drive, you can copy-paste this URL in the address bar of Windows Explorer \\ca-um-nas201.unimaas.nl\RIT-iRODS-ingestzones\prod
    • (Mac and Linux users)... Make sure to mount the SMB/CIFS network location ca-um-nas201.unimaas.nl/RIT-iRODS-ingestzones/prod
  • The data that you are uploading does not contain any personal identifiable information, such as patient names, addresses, BSN-registrations etc.



The end result will be a data set that is:

  • annotated with ontology-enriched metadata;
  • safely stored in the iRODS storage environment;
  • findable (on metadata) for all MUMC+ users;
  • accessible by the members of your project.



Instructions

If you meet the requirements listed above, you can begin uploading a new data set (also called Collection) to the DataHub infrastructure.

Click on the screenshots to enlarge them!

Step 1 - Open the portal

Point your browser to https://datahub.mumc.maastrichtuniversity.nl/
Use the menu on the right side to login with your UM- or MUMC+ credentials.

Don't forget to check the mark with the I'm not a robot Captcha.



Step 2 - Listing drop zones

Click the Preserve data item in the menu at the left side. 








On the next page, click Drop zones. 




This will generate a list of drop zones that are currently open for you. 
If it is your first time, you will see an empty screen with a parachute.  


Step 3 - Create a new drop zone and enter metadata

Click on New drop zone. This opens a new metadata entry form for this Drop zone. 
There are various fields to fill out. Some are required, some are not. The section below explains the values to enter in the various fields.


Project

Here you select the project whereto you want to upload the data set.
Should your project not be listed here, please create a new one or contact your DataHub contact person.


Title

Enter the title that best describes your data.


Description

Enter a description that best describes your data here.


Date

Enter the date on which your data set was collected / your data set was finished. (required)


Factors

Enter variables that influenced the outcome of your experiment. For example: age, gender or chemicals

  

Organism (ontology lookup)

Please enter the main organism of your data-set here. 
For example, if your dataset mainly focuses on humans, choose the term Homo Sapiens.

The autocomplete box also support the use of synonyms.  
You can also type human", rat" or mouse" (etc.) to retrieve the proper ontology terms.

This field is special because data that is entered is being enriched with information from an ontology. 
The advantage of using an ontology are:

  • Less chance of typing errors;
  • Consistent naming;
  • The ability to enrich with external knowledge and adding semantics (= machine readability) to data

For more information about ontologies, please visit wikipedia.  


Tissue (ontology lookup)

Enter the main body part on which your data set is generated. 
Examples include heart, lung or bone.


Technology (ontology lookup)

Enter the measurement technique that is primarily used in your data set.
Examples are Surgery, Western blot analysis or RNA sequencing


Related Publications (DOIs)

Define publication(s) relevant to your data set. These publications may be written by yourself, but can also contain references to third-party publications. 
Enter a valid DOI for the publication and press Add article. You can add as many related publications as you like.


Creator

Will be automatically filled based on the user that is currently logged in.


Contacts (table)

Specify contact persons for this data set. 
This is very important because people may find your data set interesting and would like to have an opportunity to contact you.


Protocol

Enter a name and file name of the protocol file that you've used to acquire this data set. This can be a lab protocol, but also instructions on data processing or calculations are possible. 
If you have a specified a filename here, you MUST copy that file into your drop zone. 




Press Submit to store the metadata information and return to the dropzones listing.




Step 4 - Access the new drop zone

By pressing Submit in step 3, you return to the listing of drop zones and will see a new card containing the information of your drop zone and most important, the internal name that this drop zone has been assigned (eg. hungry-hazel).

The metadata that you've just entered has been saved in an XML file and the new drop zone is also created on your network drive W:







Open Windows Explorer (or a similar file browser on a Mac or Linux operation system) and navigate to the W:\ network drive. You will see that the dropzone folder with the generated name (eg. hungry-hazel) appears in the listing.

Windows users without the W:\ network disk and Linux and Mac users should use the address below to access the drop zones:

  • Windows, type this in the Windows Explorer address bar \\ca-um-nas201.unimaas.nl\RIT-iRODS-ingestzones\prod
  • Linux / Mac: create a SMB-connection to ca-um-nas201.unimaas.nl/RIT-iRODS-ingestzones/prod








Step 5 - Copy data to the drop zone

Add the actual data files of this data set to the newly created dropzone folder. Data files can consist of raw data, derived data, protocols etc. Any file format is allowed. It is also possible to upload subfolders.

Just copy-and-paste or drag-and-drop the data from your local hard drive (or USB-drive) to this dropzone folder.



Step 6 - Ingest the data

When the data transfer into the dropzone has finished, you can ingest the data into the DataHub infra for persistent storage. 
To do so, choose the appropriate drop zone card (here: hungry-hazel) and click Edit







Please make sure that all the metadata is still correct and click Ingest at the very end of the form.


What happens now is that your data-set is moved from the temporary drop zone to a permanent place in the DataHub infrastructure.
Your will also see that the status of your data set changes sequentially to:

  • in queue for validation
  • validating
  • in queue for ingestion
  • ingesting
  • ingested

  

24 hours after a successful ingest, the dropzone card will disappear from the list and the drop zone will be deleted from the network drive. 



Step 7 - Retrieve the data

To browse and download the data, please follow the Methods for retrieving data guide.




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