ICAT @ ESRF

ICAT

ICAT is an open source metadata management system designed for large facilities and provided by PaNdata (consortium of all photon and neutron sources in Europe, dedicated to sharing good practices of data management). It enables the collection, storage and searching of the generic metadata of experiments along with the corresponding raw data, therefore enabling their reuse at a later stage.

It also serves the purpose of tracking all samples sent on-site for experiments to be performed at the ESRF. Before sending a parcel of samples or ancillary equipment to the ESRF, users must declare those elements in the shipment corresponding to their experiment session in ICAT, ask for safety authorisation, and print the label created by ICAT to affix to the parcel to be sent.
 

Access to the metadata and raw data - the ESRF Data Policy

Only the proposers and experiment team can access these data during an embargo period of three years after the experiment, after which time the data will be automatically made public for other users to see and use. This applies to non-proprietary research experiments only - see the ESRF Data Policy for more details and exceptions.

Automatically collected metadata for the ESRF experiments can be accessed here with your User Portal login.
 

DOI for my experiment

A DOI is automatically generated for each experiment session and should be mentioned in any publications that use data from that session.
 

Status of ICAT implementation on the ESRF beamlines

The implementation of metadata storage and data archiving on all beamlines is a big project - follow the progress and see the latest status of its implementation on the beamlines here.

More information on the ICAT project can be found here.

ICAT Sign in

Log-in to https://data.esrf.fr with your User Portal (SMIS) credentials to access your proposal data. If you log-in as anonymous you will only have access to opened data (opened after the three-year embargo period or manually released by a user).

Look for the dataset you are interested in either by using the search tool or by using the proposal number and/or beamline number. Click on “Download” to retrieve the data in a zip file.

ICAT@ESRF also serves the purpose of tracking all samples and equipment sent to the ESRF for user experiments. The ESRF is obliged to know at all times what samples and equipment are onsite, where they are at any particular time, and when they have left the site. Before sending any samples or ancillary equipment to the ESRF, users must declare those elements in a shipment corresponding to their experiment session in ICAT, request Safety authorisation, and print the label(s) created by ICAT to affix to the parcel(s) to be sent. This label allows each parcel to be tracked both by the user and by the ESRF.

ShipmentProcess.png
 

Rules and Prerequisites :
 

All sample sheets must first be created and completed in the User Portal, and validated by the Safety group before they can be added to a parcel in ICAT.

Although any scientist linked to a proposal can create a shipment and parcels in ICAT, the “Request Safety Approval” step can only be performed by a user who is listed on the A-form of the relevant experimental session.
 

1. Create a shipment for your experiment session
 

A shipment is a set of parcels to be sent for a particular experiment session. The parcels in the shipment can be sent from the same or different addresses. To create a shipment in ICAT :

  • Log-in to ICAT@ESRF (https://data.esrf.fr) by clicking on the « Sign in with ESRF SSO » button. This will use your personal ESRF credentials to log you in. If you cannot login this way, you need to first go the ESRF User Portal to create your ESRF Username (this is a new requirement since June 2020).

ICAT Sign in
 

  • You will be automatically directed to the « My Data » tab, which shows a list of all the experiment sessions scheduled for the different proposals you belong to.

Note: ICAT gets updated information regularly from the User Portal (i.e. new experiment sessions, new sample sheets). If you don’t see your session but have received an invitation, please wait for about 15 min and refresh the page.

 

  • Select the experiment session for which you wish to create a shipment by clicking on the proposal number of the session. In this example, the session taking place on ID19 on the 27/02/2020 for the proposal test123 has been selected:

Select session
 

  • Select the « Shipping »  subtab for that session.

Shipping subtab
 

2. Select/create addresses for your shipment
 

  • If this is the first parcel created for that session you will be asked to define default sending and return addresses for this shipment:

Default Shipping addresses.png

  • In the case of non pre-existing addresses:
    • You will be notified that no addresses are found. Select the « Create new shipping address » link.

      Default Shipping addresses new
       
    • After filling-in the address, click on « Create ». Newly created shipping addresses will be added to your list of addresses.
       
  • If you have pre-existing addresses:
    • You can selecte a pre-existing address from the dropdown menu:
      Select default address
       
    • Or create a new address by clicking on « Create new shipping address »:
      Default Shipping addresses new
       
  • If you don’t want your samples returned to you but prefer that they are destroyed by the ESRF after the experiment, please leave « No default return address » in the « Default return addres » field:

No default address
 

  • Click on « Save » to keep these addresses as the default ones for the shipment. Each new parcel created for this session will then have these addresses filled in automatically, but of course it will be possible to edit or modify them at the level of the individual parcel if needed.
     
  • The default shipment addresses can be modified by clicking on « Edit » on the top right hand side of the « Shipping Configuration » section:

Shipping Configuration.png
 

  • The default shipping addresses can also be created and modified on the « My Addresses » page under « Shipping » in the menu on the top of the page:

My Addresses page.png
 

This step can be by-passed if you have already done it for another parcel from the same shipment.

Important note (NOT for industrial experiments): The ESRF will reimburse the shipping costs for a certain number of parcels (http://www.esrf.fr/NonMX-RemoteExperiments, After Your Experiment, point1) – any parcels for which reimbursement is requested must be shipped from and returned to ESRF member countries.

 

3. Add your parcels to your shipment
 

  • Click on the « New Parcel » button in the « Shipping » subtab of your session.

Add New Parcel button
 

  • Each time you create a new parcel, you will be asked for a parcel Name (this is for your use only so you can find your parcel easily), the storage conditions at reception and eventual comments for ESRF staff:

Create Parcel
 

  • You can keep the addresses you selected for the shipment, or edit them by selecting a saved address from the dropdown menu « Choose » or by editing the fields manually:

Create Parcel
 

  • If you do not want your samples returned to you but prefer that they are destroyed by the ESRF after the experiment, please tick the checkbox « No return address (the parcel will be discarded) » :

No Return Address.png
 

  • Click « Create » on the bottom of the page when you have finished defining your addresses.
     
  • The new parcel will be added to the list of parcels for your shipping, and now needs to be filled with items. Click on « View » to fill in the parcel details.

New parcel in list

 

4. Add items (samples or ancillary equipment) to your parcel
 

  • On the parcel's detail page under the « Content » section, click on « Add an item ».

Add item to parcel.png
 

  • For each Item added, you will need to provide a Name and then select the item type : « Sample Sheet », « Tool » or « Other ».
  • When you select « Sample Sheet » you will be given a pull-down menu showing all the samples that you have listed in the A-form of the experiment session (only samples validated and assigned a colour by the Safety group can be added to the A-form). You can select the relevant samples for that parcel from this list.
     
  • When you select « Tool » or « Other », you must provide a description of the item.
     
  • An additional comments box is available if needed.

Add item sample sheet.png
 

Note: To avoid delays at the “Request Safety Approval” step, we recommend that you provide a clear and precise description of each item you will send.

 

5. Request Safety approval
 

  • Once your parcel is ready, you must request Safety approval to send the parcel to the ESRF.
     
  • This is done by changing its status from « SCHEDULED » to « READY FOR SAFETY CHECK » by clicking on « READY FOR SAFETY CHECK » at the top of the parcel page.

Ready for Safety Check-1.png
 

Note: only Users declared on the A-form of the experiment session can change the parcel status to « READY FOR SAFETY CHECK ».

 

  • You will be asked if the parcel contains dangerous goods; please indicate if this is the case. This information is needed for ESRF internal use only; you will still need to complete any official declarations or protocols related to the transport of dangerous goods as requested by your courier company.
     
  • A notification will be sent to the ESRF Safety group to check the parcel's content, and also to all the users on the A-form for that session.
     
  • The Safety group will either APPROVE, REFUSE, or REQUEST MORE INFORMATION for your parcel. In all cases the users on the A-form will receive a notification of the safety approval status of the parcel.

Note: Once APPROVED by the Safety group, the parcel is not editable anymore.

 

6. Print the parcel labels and send the parcel
 

ONLY once the Safety has approved the sending of the parcel to ESRF, you can prepare and send it for shipment:

  • Print the TO and FROM ESRF labels: On the parcel details page, click on the « Download Labels » button that is now accessible on the top right hand side of the page.

Donwload labels
 

Note: The QR code that appears on these labels is used for tracking your parcel when it arrives at the ESRF Stores and at the beamline, until it is sent back to you or destroyed.

 

  • Affix the "TO ESRF" label to the parcel.

Label TO ESRF-1.png
 

  • Put the Return label inside the parcel so that it can be used for returning your parcel to you.

Label FROM ESRF-1.png
 

IMPORTANT : Make sure to also request a return label from your courier company for it's seamless return to you after your experiment.

 

  • Organise the transport of your parcel with your courier company and transport adviser to make sure all the paperwork necessary for the shipment is completed and affixed to the parcel.
     
  • Send the Parcel.
     
  • Change its status in ICAT from « APPROVED » to « SENT » by clicking on the « SENT» button at the top of the parcel page. Once this is done, all users declared on the A form will receive a confirmation that the parcel has been sent, and a notification when the parcel arrives at each new location (at the ESRF Stores, at the beamline, ...).

Send Parcel.png
 

Note: Any parcels containing samples, substances or equipment sent for a user experiment and that do not display the ICAT shipping label will be destroyed, since they will not have been approved by the Safety Group for sending to, and reception by, the ESRF.

 

7. Follow the location of the parcel
 

  • Email notifications will be sent to the Users on the A-form for each modification of the parcel status.
     
  • An overview of the parcel status history is available in ICAT in the « History »  section at the bottom of your parcel's detail page.

Parcel History
 

According to the ESRF Data Policy and ESRF Publication Guidelines, every time you publish your research analysis issued from raw data measured at ESRF, you must mention the ESRF instrument on which the data were measured and include the data DOI in your manuscript in order for other scientists to reuse your data once it becomes openly accessible.

 

The DOI for a session can be found both in ICAT under the My Data tab, where you can view all the experiment sessions you have been involved in.

Use the search box to find a specific session keyword or sort your sessions by proposal, instrument or date.

Once you have found the session you are looking for, you will see the DOI link for that session in the right column of the table. Click on this link to go directly to the DOI landing page.

DOI Link in ICAT

For many publications, the data referred to in the publication are a subset of one or more experiment sessions, or include data from more than one session. For this reason, researchers may prefer to manually create a DOI for a specific collection of datasets within one or more experiment sessions.

Only Main Proposers can manually mint DOIs for a selected collection of datasets directly from the ICAT interface, by ticking the box associated to each desired dataset within the sessions that appear in the My Data tab :

Mint DOI-1.png

As soon as a dataset is selected by ticking the box, a My selection tab appears in the top black menu and all datasets ticked are added automatically to this selection.

In the My selection tab, all selected datasets can be seen, and clicking on Mint a DOI will create a DOI specifically associated to these datasets. The Main Proposer will then be asked to fill in the new DOI landing page information (Title, Abstract, Author names).

Mint DOI-2.png