Guidance – Custom ELN settings for the group

This tutorial shows Data Store Stewards (DSSts) who have been assigned the Admin role how to customise the ELN settings for their group (division / BAM-FB) in a multi-group Data Store instance based on openBIS 20.10.12.

What you will learn

Before you begin

This guidance is designed for openBIS version 20.10.12 and for DSSts with the Admin role for their group. In a multi-group instance, a designated group admin can customise Group ELN Settings for the Spaces assigned to that group without requiring Instance Admin rights.

Data Store multi-group setup: The BAM Data Store is configured as an openBIS multi-group instance. This allows multiple BAM divisions to use the same Data Store instance while maintaining division-specific Spaces and ELN settings. DSSTs therefore manage the relevant Group ELN Settings for their own division. When following this tutorial, always make sure that you have selected the correct division under Select Group Settings.

Key concepts

Data Store = openBIS multi-group instance: The Data Store uses openBIS multi-group configuration so that several BAM divisions can work in the same instance while group-specific settings and Spaces can be managed for each division.

Group ELN settings in a multi-group instance

In a multi-group openBIS instance, each configured group can have its own ELN settings. These settings control selected parts of the ELN behaviour and presentation for the Spaces belonging to that group. This allows a division to adapt the interface to its working practices while keeping centrally managed masterdata (meta-metadata: object types and controlled vocabularies) and instance-wide configuration separate.

Setting level Typical responsibility Effect
Instance settings Instance administration / system-level governance Apply to the whole openBIS instance and are not independently customised by every group.
Group settings DSSt / designated group admin Control selected ELN behaviour for the group, including templates and Object Type visibility.
Scope of this guidance: This tutorial focuses on Group ELN Settings that DSSts can use to customise how their division works in the ELN. Creating or modifying masterdata, such as Object Types, properties or controlled vocabularies, is a separate administrative task.

Tutorial workflow

To make it easier to start the self-learning path, the Data Store team has already prepared the relevant ELN group settings for the tutorial example “Material Synthesis”. In this guidance, DSSts first review these prepared settings and then learn how the same settings are created and maintained.

DSSt responsibility in normal operation: The settings used in the self-learning path are preconfigured for training purposes. For day-to-day work, these configuration steps normally need to be carried out and maintained by the DSSts for their own division. The steps below therefore explain both what has already been prepared for the tutorial and how DSSts can configure the corresponding settings themselves.
  1. Open the Group ELN Settings for your division and review the configuration prepared for the tutorial.
  2. Review the generic Object Types enabled for the tutorial and learn how to make Object Types available in ELN drop-down menus.
  3. Review the five templates supplied for the “Material Synthesis” example and learn how to create a template for a specific Object Type.
  4. Configure an Object Type to be shown in the Lab Notebook main menu.
  5. Review other group-level settings and verify the effect of your changes.

Step 1: Open your group settings

Because the Data Store is configured as a multi-group openBIS instance, first select your division to review or modify its Group ELN Settings. Use the group selector in the Settings page to open the configuration assigned to your division. In this tutorial, X.1 represents your division number.

Instructions:
  1. Open the Tools tab.
  2. Under Utilities, select Settings.
  3. Open the Select Group Settings drop-down menu.
  4. Select your division number.
  5. Click the Edit tab before changing the group configuration.
Check the selected group: Before editing, verify that you selected the correct division number. Group settings are intended to affect the Spaces assigned to the selected group.
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Step 2: Review and enable Object Types in drop-down menus

An Object Type defines a category of objects that can be registered in openBIS and determines the kind of research entity represented and the metadata structure available for that category. Examples include an experimental step, a sample, a chemical or an instrument.

For the “Material Synthesis” tutorial sequence, the Data Store team has enabled the following generic Object Types in the relevant group drop-down menus because they are used throughout the self-learning path:

New Object Types do not automatically appear in ELN drop-down menus. Use the Object Type definition extension in the Group ELN Settings to control whether an Object Type is offered in these menus.

Instructions:
  1. Open the Group ELN Settings for your division and click Edit.
  2. Open Object Type definitions Extension.
  3. Select the Object Type you want to configure.
  4. Enable Show in drop downs.
  5. Click Save.
Result: The configured Object Type can be selected in ELN drop-down menus where Object Types are offered to users in the group.
How to review which Object Types are enabled in drop-down menus:
  1. Open the Group ELN Settings for your division.
  2. Open Object Type definitions Extension.
  3. Review the configured Object Types and their settings.
  4. For each relevant Object Type, check whether Show in drop downs is enabled.
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Step 3: Review and create templates

Templates provide pre-defined values for an Object Type and can make repeated registration tasks more consistent. A group can have several templates for the same Object Type, for example different templates for Experimental Step objects.

Why Object Types come first: Every template is created for a specific Object Type. Reviewing Object Types before templates therefore makes it clearer which kind of object the template will create or pre-fill. In this self-learning path, the Data Store team has already prepared both the relevant Object Types and the tutorial templates so that DSSts can first review the setup and then learn how to configure the same settings for their own division.
Responsibility for templates: Only Data Store Stewards (DSSts) can create templates in the system. However, the information, pre-defined values and relationships included in a template should be discussed and worked out together with members of the division. This helps ensure that templates reflect actual research workflows, are meaningful to group members and are used consistently.
Instructions:
  1. Open Tools → Utilities → Settings.
  2. From Select Group Settings, select your division number.
  3. Click the Edit tab.
  4. Open the Templates section.
  5. Click + Template.
  6. Select the Object Type for which the template is intended, for example Experimental Step.
  7. Fill out the values that should be pre-defined by the template.
  8. Add parent(s) and/or child(ren) if required.
  9. Review the entries and click Save.

All templates available to your group are displayed in the Templates section of the selected Group ELN Settings.

How to get an overview of registered templates:
  1. Open Tools → Utilities → Settings.
  2. Under Select Group Settings, select your division number.
  3. Open the Templates section.
  4. Review the templates displayed for the selected group. You do not need to create a new template.

Templates prepared for the “Material Synthesis” tutorial example

For the self-learning path, the Data Store team has already provided five templates for each group. These templates represent the main stages of the tutorial workflow and allow DSSts to review how pre-defined Experimental Step structures can support consistent documentation.

  1. Material Synthesis
  2. Chemical Treatment
  3. Macrostructure Characterization
  4. Microstructure Characterization
  5. Microstructure data analysis
Synthetic tutorial data: The information pre-filled in the five templates provided for the “Material Synthesis” tutorial example is synthetic training data. It is designed only to demonstrate Data Store functions and the self-learning workflow and does not aim to be scientifically correct or suitable for real research documentation.
Parent and child relationships: Applying a template does not replace Parent and child relationships that are already assigned to the Object. Existing relationships are retained, and parent(s) and child(ren) defined in the Template are added to them.
Masterdata definition process and related concepts . Back to top

Step 4: Show Object Types in the Lab Notebook menu

Object Types can also be configured to appear in the Lab Notebook section of the main menu. In the standard ELN configuration, Entry and Experimental Step are displayed there by default.

Instructions:
  1. Open the Group ELN Settings for your division and click Edit.
  2. Open Object Type definitions Extension.
  3. Select the relevant Object Type.
  4. Enable Show in lab notebook main menu.
  5. Click Save.
Lab Notebook versus Inventory: The Show in lab notebook main menu option is intended for the Lab Notebook. Inventory objects are generally handled through their Inventory Spaces, Projects, Collections and object tables rather than by adding every Inventory Object Type to the main menu.
How these settings are used by group members: Object Types and templates become visible to users when they register objects in the Lab Notebook and in the Inventory. Object Types determine which kind of object can be registered, while templates can provide pre-defined values and relationships for supported Object Types. Their practical use will become clearer in the follow-up tutorials of this self-learning path, where users create and connect objects for the “Material Synthesis” example.
How to review which Object Types are enabled in the Lab Notebook menu:
  1. Open the Group ELN Settings for your division.
  2. Open Object Type definitions Extension.
  3. Review the configured Object Types and their settings.
  4. For each relevant Object Type, check whether Show in lab notebook main menu is enabled.
  5. Verify the result in the Lab Notebook main menu, where the enabled Object Types are displayed.
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Step 5: Customize the Main Menu

The Main Menu settings control which Data Store functions are displayed to users of the selected group. For the self-learning path, review the configuration prepared for your division and confirm that all of the functions listed below are enabled.

Instructions:
  1. Open Tools → Utilities → Settings.
  2. Under Select Group Settings, select your division number.
  3. Click the Edit tab.
  4. Open the Main Menu settings section.
  5. Review the available Main Menu options.
  6. Confirm that each of the following options is enabled for your group:
    • showLabNotebook
    • showInventory
    • showObjectBrowser
    • showExports
    • showStorageManager
    • showAdvancedSearch
    • showTrashcan
    • showVocabularyViewer
    • showUserManager
    • showUserProfile
    • showBarcodes
    • showDatasets
  7. If one or more required options are disabled, enable them.
  8. Review the configuration and click Save if you made changes.
How to review the result: After saving, return to the Data Store interface and review the Main Menu. The enabled functions should be available to users of the group, subject to the permissions and functionality configured for their accounts.
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Other group settings

Group ELN Settings that can be customized by DSSts.

Group setting Purpose
Storages Create and configure storage structures used by the group where storage functionality is enabled.
Object Type definitions Extension Extend ELN behaviour for Object Types, including visibility in drop-downs and the Lab Notebook main menu and, settings for parent and child relationships.
Main menu Adjust selected menu behaviour so that the group's navigation reflects the workflows used by the division.
Group settings are not masterdata: Divisions can define new Object Types when required to represent or map their research workflows in the Data Store. This process is called masterdata definition and includes the definition of Object Types and controlled vocabularies. Masterdata work is coordinated by DSSts within the divisions together with the Data Store team. The BAM data model work task force coordinates the definition of BAM masterdata with the aim of creating a coherent data model that makes BAM research data reusable within BAM and across the relevant scientific disciplines.

When to start: The recommended time to begin the masterdata definition process is after a division has completed the Data Store self-learning path and starts implementing its own use cases. Masterdata definition is therefore not part of Data Store onboarding; it belongs to the subsequent rollout process, when division-specific research workflows and metadata requirements can be translated into appropriate Object Types and controlled vocabularies.

For details, see the Data Store wiki page: Masterdata definition process and related concepts .

Result

After completing this guidance, you should be able to open your division-specific Group ELN Settings, create templates, enable Object Types in drop-down menus, and control which Object Types are displayed in the Lab Notebook main menu.

Before you finish:

Sources

openBIS

Data Store Wiki