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 User manual


Introduction

This user manual will guide you through the process of uploading data to the Maastricht Data Repository (MDR) via the drop zones method. 

Before you start!

Prerequisites and general conditions for uploading new data are: 

  1. You have been assigned a project from the DataHub intake interview. If not, please refer to this page: Starting a new project
  2. You are connected to the UM- or MUMC-network. Either physically or via VPN.
  3. You are using a compatible web browser (Chrome or Firefox recommended)
  4. You have an UM- or MUMC-account
  5. The data that you are uploading does not contain any personal identifiable information, such as patient names, addresses, BSN-registrations etc.
  6. You have the drop zones network drive mounted:

     Instructions UM

    Windows users 

    1. The network drive W:\ should be visible from Windows Explorer - My Computer.
    2. 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

    1. Make sure to mount the SMB/CIFS network location ca-um-nas201.unimaas.nl/RIT-iRODS-ingestzones/prod
     Instructions MUMC

    Windows users 

    1. Copy-paste this URL in the address bar of Windows Explorer \\researchitrc04.prd.corp\resitcachprod

    Mac and Linux users

    1. Make sure to mount the SMB/CIFS network location researchitrc04.prd.corp/resitcachprod



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 Maastricht Data Repository.

Click on the screenshots to enlarge them!

Step 1 - Open MDR

Point your browser to https://mdr.datahubmaastricht.nl/
Use the menu on the left side to login with your UM- or MUMC+ credentials.


Step 2 - Listing drop zones

Click the Preserve data item to expand the menu at the left side and click Drop zones.




This will display the list of active drop zones for your account. 
If no active drop zones can be found, for instance because this is your first time visiting MDR, only the "Create new drop zone" button is shown. 



There are 2 active drop zones for this account

This user does not have any drop zones yet.



Step 3 - Create a new drop zone and enter metadata

Click on Create new drop zone. This opens a new metadata entry form. 
There are various fields to fill out. Some are required, some are not. More information about each field in the form can be found in the section below (click Read more).


 Click here to read more about the metadata fields...

*Project

(required field) Here you select the project to which you want to upload the data set.
Should your project not be listed here, please request a new data project or contact your DataHub contact person.


*Title

(required field) Enter the title that best describes your data.


Description

Write a description that best describes your data here. This text block supports multiple lines.


*Date

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


*Creator

(required field) Your e-mail address is automatically entered in this field.

 

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


Factors

Enter variables that influenced the outcome of your experiment. You can also use this field for entering keywords. For example: age, gender or chemicals


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.


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.



After entering the metadata, press Submit to store the metadata information and return to the drop zones 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 your file browser (i.e. Windows Explorer) and navigate to the W:\ network drive. You will see that the drop zone folder with the generated name (eg. hungry-hazel) appears in the listing.

If you don't have a W:\ network disk, you can use these direct links to access the drop zones:

 Instructions UM

Windows users 

  1. Copy-paste this URL in the address bar of Windows Explorer \\ca-um-nas201.unimaas.nl\RIT-iRODS-ingestzones\prod

Mac and Linux users

  1. Make sure to mount the SMB/CIFS network location ca-um-nas201.unimaas.nl/RIT-iRODS-ingestzones/prod
 Instructions MUMC

Windows users 

  1. Copy-paste this URL in the address bar of Windows Explorer \\researchitrc04.prd.corp\resitcachprod

Mac and Linux users

  1. Make sure to mount the SMB/CIFS network location researchitrc04.prd.corp/resitcachprod









UM drop zones


MUMC drop zones


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 drop zone has finished, you can ingest the data into Maastricht Data Repository for persistent storage. 
To do so, choose the appropriate drop zone card (here: silly-toad) and click the blue pencil icon to continue.







Optional: if you just want to save the changed metadata and not start the ingest operation yet, click Save drop zone.

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

A message pops up asking for confirmation. Click Start ingest.



What happens now is that your data set is moved from the temporary drop zone to a permanent location in the Maastricht Data Repository.
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 drop zone 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 User manual: Methods for retrieving data guide.