Upload data in the Lab Notebook

This tutorial shows division members how to organize and document research data in the Lab Notebook of the Data Store using the synthetic “Material Synthesis” example. You will create a Project and Collections, register Experimental Steps manually and using templates, upload datasets, and use filtering and search functions to locate registered information.

What you will learn

Before you begin

This tutorial is designed for openBIS version 20.10.12 and does not require prior experience with openBIS.

Before starting this tutorial, you must:

Tutorial sequence

This tutorial introduces the Lab Notebook part of the synthetic “Material Synthesis” example. The Experimental Steps and datasets registered here will later be connected with Instrument, Chemical, and Sample objects registered in the Inventory.

Key concepts

Lab Notebook

In the Lab Notebook, each user has a personal workspace (Space in openBIS) for organizing research projects, experiments, simulations, analyses, and other activities that generate research data.

Research activities can be represented as Experimental Steps organized within Collections of a Project. Datasets should be attached to the Experimental Step that describes how the corresponding data was generated. Experimental Steps can also be connected with other Experimental Steps and related Inventory objects, such as instruments, chemicals, software, and samples, using parent-child relationships.

These connections make it possible to represent research workflows and document the provenance of research data in the Data Store.

Overview of the Material Synthesis project in the Lab Notebook
The Material Synthesis Project will be created in the user's Home Space and contains all th Collections that organize the Experimental Steps used for the tutorial example.

Lab Notebook structure for "Material Synthesis"

The tutorial example "Material Synthesis" uses the Data Store hierarchy Space → Project → Collection → Object → Dataset. In the Lab Notebook, research activities are represented as Experimental Step objects and datasets are attached to the corresponding Experimental Steps.

In this tutorial, you will work within your User Space in the Lab Notebook. You will register a Project, Collections, and Experimental Steps, and attach datasets to the corresponding Experimental Steps. In follow-up tutorials, you will register the corresponding Inventory items and connect them with these Experimental Steps to represent the complete research workflow in the Data Store.

Data organization: openBIS 20.10.12 also supports folders and subfolders. However, the Data Store recommends primarily organizing research information using the core structure Project → Collection → Object → Dataset. Collections, metadata, and parent-child relationships provide a consistent and scalable way to organize and connect research information while keeping the Lab Notebook navigation concise.
Data Store data model showing Experimental Steps and datasets in the Lab Notebook
Experimental Steps are represented as objects, organized in Collections within the Material Synthesis Project. Datasets are attached to the Experimental Steps that describe how they were generated. Entities outlined in red represent the Lab Notebook structure and objects that you will create in your User Space during this tutorial.

Tutorial workflow

  1. Create the Project and Collections used to organize the “Material Synthesis” example.
  2. Register Experimental Steps manually and using predefined templates.
  3. Edit the prepared structure and register the remaining Experimental Steps.
  4. Upload research data as datasets and review the uploaded data.
  5. Filter registered Experimental Steps and create an Advanced Search query.

Step 1: Register a Project

Create a Project in the Lab Notebook to represent the research project Material Synthesis.

Instructions:
  1. Select the upper LAB NOTEBOOK tab.
  2. In the left-hand navigation menu, select Home Space.
  3. Click + Project.
  4. Enter Code: MATERIAL_SYNTHESIS.
  5. Enter the following Description: This tutorial project demonstrates a simplified workflow for the synthesis and characterization of a material within openBIS. The experimental descriptions, metadata, and datasets are synthetic example data created solely for training and demonstration purposes.
  6. Review all entries and click Save.
Lab Notebook interface showing how to create a project
Select Home Space in the Lab Notebook and use + Project to open the project-registration form.

General information

Mandatory fields in openBIS are marked with an asterisk (*). Project codes should be meaningful and should follow the naming conventions agreed for the Data Store. Once saved, a project code cannot be modified or reused.

Identification information: If the Code or Description fields are not displayed, open the More drop-down menu and select Show Identification Info.
More menu showing Show Identification Info
Use More → Show Identification Info to display hidden identification fields.
Project registration form with Save action
Enter the Project Code and Description, review the entries, and click Save.
Saved Material Synthesis project shown in Home Space
The newly registered Project is displayed under Home Space in the left-hand navigation menu.

General information: Project access

Access in openBIS can be managed at the Space and Project levels. Permissions assigned to a Project are inherited by its Collections, Objects, and Datasets.

For collaborative work within or across divisions, use a dedicated Project and assign the appropriate Observer, User, or Admin role to the required users or groups. For more information, see roles and rights in the Data Store .

Back to top

Step 2: Register Collections

Collections organize related Experimental Steps and other research activities within a Project. In this tutorial, you will create five Collections for the “Material Synthesis” workflow.

Instructions:
  1. Select the Material Synthesis Project.
  2. Click + Other.
  3. Select Collection.
  4. Leave the autogenerated Code (*) unchanged.
  5. Enter Synthesis as the Collection Name.
  6. Leave Default object type empty.
  7. Select List view as the Default Collection View.
  8. Review all entries and click Save.
Repeat the procedure to create the following additional Collections: Treatment non-destructive, Structure_TEM, Parameter 1, and Parameter 2.
Material Synthesis project view showing collection creation
Select the Material Synthesis Project and click + Other.
Select Collection type window
In the type-selection window, select Collection.
Collection registration form
Leave the autogenerated Code unchanged, enter the Collection Name, leave Default Object Type empty, select List View, and save the Collection.
Overview of registered collections
The registered Collections are displayed under the Material Synthesis Project.
Context menu for changing collection sorting
Open the Project context menu and select Change sorting to modify the display order of Collections.
Sorting options for collections
Select a sorting option, for example Registration Date Ascending.
Back to top

Step 3: Register an Experimental Step

Research activities that generate data, such as experiments, measurements, simulations, or analyses, can be represented in openBIS as Experimental Steps.

Instructions:
  1. Navigate to the Synthesis Collection.
  2. Select More → New Object.
  3. Click Select an object type.
  4. Select Experimental Step.
  5. Leave the autogenerated Code unchanged.
  6. Enter Material Demo 001 as the Name.
  7. Complete all mandatory (*) and other relevant properties.
  8. Review all entries and click Save.

General information

More menu showing New Object
In the Synthesis Collection, select More → New Object.
Experimental Step object type selection
Select Experimental Step as the Object Type.
Experimental Step registration form
Enter Material Demo 001 as the Name, complete the mandatory properties (*), and save the Experimental Step.
Back to top

Step 4: Register an Experimental Step using a Template

Templates help standardize metadata and reduce repeated manual data entry when similar Experimental Steps are registered.

Instructions:
  1. Navigate to the Synthesis Collection.
  2. Select More → New Object.
  3. Select the Object Type Experimental Step.
  4. Open the Templates tab.
  5. Select the template Material Synthesis.
  6. Leave Merge current parents/children disabled.
  7. Click Accept.
  8. Leave the autogenerated Code unchanged.
  9. Enter Material Synthesis as the Name.
  10. Enter Start Date and End Date using the calendar selector.
  11. Enter a comment in the Comments section.
  12. Review all entries and click Save.
Templates: Templates must be created for a specific Object Type before they are available for selection. In the Data Store, template configuration is performed by users with Group Admin rights, typically Data Store Stewards.
Template behavior: A template can only be selected during object creation; it cannot be applied retrospectively to an existing object. If a template contains parent-child relationships that need to be combined with relationships already present, use Merge current parents/children.
More menu for creating a new Experimental Step
Select the Collection and choose More → New Object.
Experimental Step object type selection
Select Experimental Step as the Object Type.
Templates tab with Material Synthesis template
Open the Templates tab and select the Material Synthesis template.
Experimental Step form populated from template
Complete the required values and save the Experimental Step.
Registered Experimental Step shown in the collection
The registered Experimental Step is displayed in the selected Collection.
Back to top

Step 5: Edit Collections and Objects

Consistent naming helps maintain a clear overview of registered Projects, Collections, Objects, and Datasets. In this step, you will rename one Collection and delete one Experimental Step.

Exercise: Edit a Collection

Instructions:
  1. Select the Collection Structure_TEM.
  2. Select More → Edit Collection.
  3. Open the Edit tab.
  4. Change the Name to Parameter 2 Analysis.
  5. Review the entry and click Save.
  6. Refresh the page if the updated name is not displayed immediately.
More menu showing Edit Collection
Select the Collection and choose More → Edit Collection.
Edit tab for a collection
Open the Edit tab to modify the Collection Name.
Updated collection name
Change the Name to Parameter 2 Analysis and save.

Exercise: Delete an Experimental Step

Instructions:
  1. Navigate to the Synthesis Collection.
  2. Select Material Demo 001.
  3. Click the DELETE tab.
  4. Enter a value in the mandatory Reason (*) field.
  5. Leave Delete also all descendants unchecked.
  6. Click Accept and confirm the deletion.
  7. Return to the Collection and confirm that the object is no longer listed.
Delete tab for an Experimental Step
Select Material Demo 001 and open the DELETE tab.
Deletion reason field
Enter a mandatory deletion reason and leave descendant deletion unchecked.
Delete confirmation
Review the deletion settings and confirm the deletion.
Deletion: Deleting descendants may also remove connected objects and attached datasets. If you only want to remove the selected object, leave the descendant-deletion option unchecked.

General information: Restore deleted objects

Deleted objects are moved to the Trashcan, where they can be restored or permanently deleted.

Trashcan and Operations menu
Open TOOLS → Trashcan, select a deleted object, and use the Operations menu to view available actions.
Permanent delete operation in Trashcan
Permanently deleted objects cannot be restored.
Back to top

Step 6: Register additional Experimental Steps using Templates

Register five additional Experimental Steps using the same template-based procedure introduced in Step 4.

Instructions:
  1. Navigate to the Collection listed in the table below.
  2. Select More → New Object.
  3. Select the Object Type Experimental Step.
  4. Open the Templates tab.
  5. Select the corresponding Template.
  6. Leave Merge current parents/children disabled.
  7. Click Accept.
  8. Leave the autogenerated Code unchanged.
  9. Enter the corresponding Experimental Step Name.
  10. Enter Start Date and End Date.
  11. Enter a comment.
  12. Review all entries and click Save.

Values for each Experimental Step

Experimental Step Collection Name Template Name Experimental Step Name
1 Treatment non-destructive Chemical Treatment Chemical Treatment
2 Parameter 1 Macrostructure Characterization Macrostructure Characterization
3 Parameter 1 Macrostructure Characterization Macrostructure Characterization TS
4 Parameter 2 Microstructure Characterization Microstructure Characterization
5 Parameter 2 Analysis Microstructure data analysis Microstructure data analysis

Exercise: Review the registered Experimental Steps

Instructions:
  1. Select the Material Synthesis Project.
  2. Select More → Show Overview if the overview is hidden.
  3. Review the registered Experimental Steps in the Objects section.
  4. Scroll horizontally to review properties such as Collection, Registrator, Registration Date, and Modification Date.
Project overview command
Open the Project and select More → Show Overview.
Project overview showing registered Experimental Steps
Review the registered Experimental Steps and their properties in the Project overview.
Back to top

Step 7: Upload Data

The Data Store recommends attaching datasets directly to the Experimental Step that describes how the data was generated. Uploaded files are stored in openBIS as Datasets.

Download the tutorial datasets

Download the following files before starting the upload exercises. Keep Parameter1_Macroscopic.zip compressed. The files contained in datasets.zip will be used individually in the subsequent exercises.

Download Parameter1_Macroscopic.zip

Download datasets.zip

Exercise: Upload Raw Data

Instructions:
  1. Navigate to Parameter 1.
  2. Select Macrostructure Characterization.
  3. Click + Dataset.
  4. Select Raw Data as Dataset Type.
  5. Enter Parameter 1 raw as Dataset Name.
  6. Enter Synthetic example images for demo purpose as Comments.
  7. Select Parameter1_Macroscopic.zip.
  8. Wait until the upload completes successfully.
  9. Enable Uncompress before import.
  10. Review all entries and click Save.
Macrostructure Characterization Experimental Step
Open the Experimental Step to which the dataset will be attached.
Add Dataset action
Click + Dataset to register a new dataset.
Dataset upload form
Enter Dataset Type, Name, and Comments, then upload the dataset file.
Dataset Save action
Review the entries and click Save.
Uploaded dataset shown in Experimental Step
Uploaded datasets are displayed within the corresponding Experimental Step.

Exercise: Upload an ELN Preview

Instructions:
  1. Open Macrostructure Characterization in Parameter 1.
  2. Click + Dataset.
  3. Select ELN Preview as Dataset Type.
  4. Enter Synthetic image1 as Dataset Name.
  5. Enter the tutorial comment.
  6. Select Synthetic-image1.png.
  7. Wait for the upload to complete and click Save.
ELN Preview dataset registration
Register the image using Dataset Type ELN Preview.
Image displayed in ELN Preview
ELN Preview datasets are displayed directly in the Experimental Step preview.

Exercise: Upload an Attachment

Instructions:
  1. Open Macrostructure Characterization.
  2. Click + Dataset.
  3. Select Attachment as Dataset Type.
  4. Enter README Synthetic image1 as Dataset Name.
  5. Enter the tutorial comment.
  6. Select README-Synthetic-image1.txt.
  7. Wait for the upload to complete and click Save.
Attachment dataset registration
Upload the README file using Dataset Type Attachment.

General information: Dataset Types

Back to top

Step 8: Filter and Search

Collections can be filtered by displayed properties and property values. Advanced Search can be used to locate specific Objects or Datasets across openBIS.

General information: Filter a Collection

Columns tab in a Collection
Use the COLUMNS tab to select displayed properties.
Column filters in a Collection
Apply filters to individual columns to locate matching objects.

Exercise: Advanced Search

Instructions:
  1. Select TOOLS → Advanced Search.
  2. Select Search For: Dataset.
  3. Select the AND operator.
  4. Define the first criterion: Field Type: All, Field Value: synthetic.
  5. Add a second criterion: Field Type: Property, Field Name: Modification Date, comparator thatIsLaterThanOrEqualTo (Date), and select the tutorial date.
  6. Add a third criterion: Field Type: Property, Field Name: Registrator, comparator thatEqualsUserId, and select your user.
  7. Run the search.
  8. Save the query as Datasets-synthetic.
Advanced Search query
Configure the search criteria and execute the Advanced Search query.
Save Advanced Search query
Save the configured query for future use.

Reuse a saved search

Instructions:
  1. Select TOOLS → Advanced Search.
  2. Select Datasets-synthetic from the saved-query list.
  3. Run the search to display the results.
Saved Advanced Search query
Select a saved query in Advanced Search and run it again.
Back to top

Result

After completing this tutorial, you should be able to organize research activities in the Lab Notebook using Projects, Collections, and Experimental Steps; register Experimental Steps manually and using templates; edit registered information; upload and associate datasets with the corresponding Experimental Steps; and use filtering and Advanced Search to locate registered research information.