Connect Lab Notebook data with Inventory items

Key concepts

Parent-child relationships

Objects in the Data Store can be connected using parent-child relationships. For research-data traceability, these relationships can link Experimental Steps in the Lab Notebook with the resources used during an activity and with the outputs generated by that activity. Datasets remain attached to the Experimental Step that describes how they were generated.

Instrument / Chemical / input Sampleresource or input object

→

Experimental Stepactivity recorded in the Lab Notebook

→

Sample / next Experimental Stepresearch output or downstream activity

Datasetattached to the Experimental Step that generated it

openBIS parent-child relationships describe a directed connection between registered openBIS Objects. The terms parent and child therefore do not have the same meaning as in programming languages, where they often describe inheritance, class hierarchies, or ownership in a software structure. In the Data Store, these links are implemented using openBIS parent-child relationships to represent how research Objects are related. Decide which Object is the parent and which is the child before saving or batch-updating a relationship. A useful convention for this tutorial is to represent resources and inputs as parents of an Experimental Step, and generated Samples or downstream Experimental Steps as its children.

In the “Material Synthesis” example, the logical connections drawn in the research workflow are implemented in openBIS as parent-child relationships. The direction of each arrow helps determine which Object is the parent and which is the child: resources and input Samples point toward the Experimental Step in which they are used, while an Experimental Step points toward the Sample or downstream activity it generates.

Research workflow for the Material Synthesis example showing logical connections between objects — Research workflow for the **“Material Synthesis”** example. The arrows connecting the activities, resources, datasets and other research outputs represented in the Data Store represent the connections that describe the research workflow and the parent-child relationships used to make the provenance of each component traceable.

Parent-child hierarchy graph generated in openBIS

Once parent-child connections have been assigned between Objects in the Data Store, openBIS can visualise them as a Hierarchy Graph. The graph is the openBIS visualisation of the directed connections that were first shown conceptually as unidirectional arrows in the “Material Synthesis” data model. Each node in the graph is an openBIS Object, and each connection corresponds to an Object-to-Object parent-child relationship.

For example, the Synthesis Instrument and the Chemicals Chemical 1 and Chemical 2 appear upstream of the Material Synthesis Experimental Step, while the generated Synthesized Material Sample appears downstream. If that Sample is later used in another Experimental Step, the graph can continue through that downstream activity and show a larger part of the research workflow.

What the graph contains: The Hierarchy Graph visualises only parent-child relationships between Objects. Datasets are not displayed as nodes. A dataset remains attached to the Experimental Step that describes how it was generated. To understand a dataset in context, open its Experimental Step and inspect the Object hierarchy around that step.

The Hierarchy Graph is therefore the software view of the same research logic shown in the workflow: conceptual arrows become stored Object-to-Object parent-child connections that can be inspected in the Data Store.

Hierarchy Graph generated in openBIS for the Material Synthesis example — Hierarchy Graph generated in openBIS for the **“Material Synthesis”** example. The graph visualises the parent-child relationships between Objects after the research workflow has been implemented in the system at the end of this tutorial. It can be used to inspect the genealogy of connected Experimental Steps, Samples, Instruments, Chemicals, and other Objects. **Datasets are not displayed in the Hierarchy Graph** because the graph visualises Object-to-Object parent-child relationships.

Traceability through connected objects

The value of these connections becomes clear when researchers need to reconstruct what happened to a Sample or understand how a dataset was generated. The following use cases show how the parent-child relationships support traceability in practice.

Use case 1: What was done with a Sample, and who generated it?

The Co-responsible person property helps identify the Sample associated with the researcher’s work. The connected Experimental Step provides the provenance needed to determine how that Sample was generated.

After opening the correct Sample Object, the researcher can follow its parent-child connections. The upstream connection points back to the Material Synthesis Experimental Step that generated it. From that Experimental Step, the researcher can continue upstream to see which resources were involved—for example the Synthesis Instrument and the Chemicals Chemical 1 and Chemical 2. If the Sample was later used in another Experimental Step, its downstream connection shows what was subsequently done with it.

In this way, the Sample Object becomes an entry point for answering practical questions such as: Who was responsible for this Sample? Which experiment generated it? Which resources were used? Was the Sample used again later, and in which activity?

Use case 2: How was this dataset generated, and can the process be reproduced?

Now imagine that a researcher finds a dataset in the Lab Notebook and wants to understand how it was produced. The dataset itself is not part of the parent-child hierarchy. Instead, it is attached to the Experimental Step that describes the activity through which the data were generated. The researcher therefore starts with that Experimental Step and follows its connected Objects.

For the dataset(s) attached to the Macrostructure Characterization experimental step, the researcher can identify the Instrument, the Samples and up-stream Experimental Stepsconnected as parents. The Experimental Step metadata, its attached dataset, and the connected Objects together provide the context needed to understand how the data were produced.

This connected context can support reproducibility by helping another researcher identify the same kinds of inputs, resources, and outputs; it can support standardization by making it easier to compare whether repeated experiments follow the same documented workflow; and it can support other downstream processes such as review, quality assurance, reuse, or preparation of research outputs.

Traceability principle: Use datasets to identify the Experimental Step that generated the data, and use parent-child connections between Objects to reconstruct the corresponding research workflow. Use Sample metadata such as Co-responsible person to identify the correct physical or material output before tracing its upstream and downstream connections.

Connections for “Material Synthesis”

The tutorial example combines Experimental Steps from the Lab Notebook with Instrument, Chemical, and Sample Objects in the Inventory. In the Data Store setup, FB (Fachbereich) corresponds to a division, which is represented as a group in openBIS. The relevant Inventory structure includes Instruments in the BAM Inventory and Chemicals and Samples in the FB Inventory. In the tutorial paths, X.1 is a placeholder for your division number. Replace it with the number of your own division when following the instructions.

Now that the research workflow has been translated into parent-child relationships, this section identifies the Objects that need to be connected. The following order is a practical way to implement those relationships after the Experimental Steps and Inventory items have been registered.

Recommended order for creating connections:

Once the relevant Objects have been registered, it is helpful to connect them in an order that follows how the research workflow is done. For the “Material Synthesis” example, and for many other research workflows, the following sequence provides a practical approach:

Register Experimental Steps and attach datasets in your Lab Notebook Space or in a Space dedicated to the specific research project. This establishes the activities that generated the research data.
Register Inventory items in the Inventory structure agreed within your group, for example Instruments, Chemicals, and Samples. This establishes the resources, inputs and outputs that need to be traced across research activities.
Connect outputs such as Samples to upstream and downstream Experimental Steps. This links the activity that generated a Sample with the later activities in which that Sample is used.
Connect Experimental Steps to other Experimental Steps where one activity directly depends on or follows another activity in the workflow.
Connect Inventory items to the Experimental Steps in which they were used, so that relevant Instruments, Chemicals, and other resources can be traced together with the data-generating activity.

This order is not a technical requirement of openBIS. It is a practical modeling strategy that helps users build the relationship network from the research workflow outward: first activities and datasets, then shared resources and outputs, and finally the parent-child connections that make the workflow traceable.

Role in workflow	Object type	Tutorial examples	Typical relationship direction
Resources	Instrument	Synthesis; Macrostructure; Microstructure	Instrument → Experimental Step
Resources / inputs	Chemical	Chemical 1; Chemical 2; Treatment Solution	Chemical → Experimental Step
Activities	Experimental Step	Material Synthesis; Chemical Treatment; Macrostructure Characterization; Microstructure Characterization; data-analysis steps	Input object → Experimental Step → output object
Research outputs / later inputs	Sample	Synthesized Material and the additional Samples registered in the Inventory tutorial	Experimental Step → Sample; Sample → downstream Experimental Step when reused

Modeling principle: represent and connect only objects that are relevant to understanding how the research data were generated. The goal is not to connect every object to every other object, but to represent the meaningful sequence of resources, activities, and outputs to trace generated research datasets.

Tutorial workflow

Connect one Experimental Step manually to learn how parent-child relationships are represented.
Batch-update the Sample objects from the same Collection to add their workflow relationships.
Batch-update objects from different Collections to add the workflow relationships of all other objects.
Visualise the Hierarchy Graph (or Hierarchy Table) of an Experimental Step to review the traceability of the workflow datasets and other outputs such as samples.

Step 1: Connect one Experimental Step

Start with one Experimental Step so that you can review the direction of each relationship before updating multiple objects. Use the Material Synthesis Experimental Step from the Synthesis Collection.

Identify the Objects to connect

In this step you will connect the Material Synthesis Experimental Step with three parents and one child. The parent and child Objects must reflect the research workflow represented for Material Synthesis, the Instrument and Chemicals used by the activity are parents, while the Sample generated by the activity is a child

In the workflow figures used in Steps 1–3, a red square highlights the Objects and relationships addressed in the current step.

Start by identifying the Objects involved in this step and the direction of each parent-child relationship. Use the workflow figure first, then confirm the exact relationships in the table below.

Connect one experimental step — Objects and relationships addressed in Step 1. The **red square** highlights the **Material Synthesis** Experimental Step and the Objects that will be connected manually in this step.

Relationships to add to the Experimental step “Material Synthesis”

Relationship	Object type	Object Name	Role in the workflow
Parent	Instrument	Synthesis	Instrument used during the Experimental Step
Parent	Chemical	Chemical 1	Chemical used during the Experimental Step
Parent	Chemical	Chemical 2	Chemical used during the Experimental Step
Child	Sample	Synthesized Material	Sample generated by the Experimental Step

Before editing the Experimental Step, determine the Name or Code of every Object that you want to connect. This tutorial illustrates two ways to do this.

Option 1: You know the Object name

When you already know the Object name, and this is unique, you can use openBIS auto-completion while assigning the relationship. In this example, add the Instrument Synthesis and the Chemicals Chemical 1 and Chemical 2 as parents.

Option 2: Find the Code to identify the object to connect

The child of the experimental step Material Synthesis is the Sample Synthesized Material that you registered in the previous tutorial “Register inventory items”. Because all division members registered Samples with the same names, the Name alone is not sufficient to identify your Sample. Filter the Samples Collection using the Co-responsible person property and then note the Code of your Sample.

In the following instructions, replace X.1 with your division number.

Filter the Samples Collection and find your Sample Code:

Select the upper Inventory tab.
Navigate to FB Inventory → X.1 Materials → SAMPLES_SYNTHESIS → Samples.
Select the Samples Collection.
Click FILTERS and select Filter Per Column.
In the property field for Co-responsible person, enter your username.
Review the filtered results and locate Synthesized Material.
Note or copy the Code of your Sample. You will use it when adding the Sample as a child of the Experimental Step.

Collection filtering:Sample names may not be unique. For example, multiple members of a division working on the same project may register Samples with the same descriptive name. Although consistent naming conventions are useful, relying on names alone can make it difficult to identify the correct Sample. A more robust approach is to use Sample Properties, such as Co-responsible person , to filter the Collection and distinguish the Sample associated with your work. Once you have located the correct Sample, use its Code or Identifier when you need to reference it unambiguously.

Filter samples collection — Navigate to the **Samples** collection in the inventory. Filter by **Co-responsible person** using your username to loacate your **Synthesized Material** and identify its **Code**.

Add all parents and children to the Experimental Step

Parent-child relationships can be assigned to an Experimental Step or any other Object from the Object's Edit tab. Add all relationships listed above in one editing session and save once after you have reviewed the complete set.

Instructions:

Select the upper LAB NOTEBOOK tab.
Navigate to your User Space → Material Synthesis Project → Synthesis Collection.
Open the Material Synthesis Experimental Step and select the Edit tab.
In the Parents section, click Search Any.
Select Instrument as the Object Type. In the Code/Name field, start typing Synthesis, wait for auto-completion, and select the Synthesis Instrument.
In the Parents section, click Search Any again. Select Chemical as the Object Type and add Chemical 1.
Repeat the previous step to add Chemical 2 as a parent.
In the Children section, click Search Any.
Select Sample as the Object Type. In the Code/Name field, enter the Code of the Synthesized Material Sample that you previously identified using your username as the Co-responsible person value, and select the Sample.
Before saving, verify that the Material Synthesis Experimental Step has the following relationships:
- Parents: the Synthesis Instrument, Chemical 1, and Chemical 2.
- Child: your Synthesized Material Sample.
Click Save.
Reopen the Material Synthesis Experimental Step and confirm that the three parents and the child are displayed correctly.

Register the connections

Open experimental step — In the Lab Notebook, open the **Material Synthesis** Experimental Step.

Edit experimental step — Click on the **Edit** tab to display the object form with parent and child sections.

Locate parents and children sections — Locate the **Parents** section, click on **Search Any**, use the **select an Object Type** field with auto-completion to add **Instrument**.

Select object type — use the **Code/Name** field with auto-completion and start typing **Synthesis** as parent.

Confirm relationships for parents — Confirm that instrument **Synthesis**, **Chemical 1** and **Chemical 2** are added as parents.

Confirm relationships for children and save — Confirm the sample **Synthesized Material** with your name as **Co-responsible person** is added as a child and `Save`.

Step 2: Batch-update Samples from the same Collection

The Sample objects registered in the previous Inventory tutorial are located in the same Samples Collection. Instead of editing each Sample separately, export the metadata of the samples to update, edit the exported Excel file to add parent-child relationships and use it for XLS Batch Update Objects.

Identify the Objects to connect

In this step you will connect the Synthesized Sample with its two children Material Sample 001 and Material Sample 002.

Identify the Samples involved in this step and confirm their relationship in the workflow before preparing the batch update.

Relationships to add to the sample "Synthesized Material"

Relationship	Object type	Object Name	Role in the workflow
Child	Sample	Material Sample 001	A sample or fraction of the Synthesized Material
Child	Sample	Material Sample 002	A sample or fraction of the Synthesized Material

Only objects from the same collection can be batch updated:

The XLS Batch Update Objects function can only be used to update objects that are located in the same Collection. If you need to update objects from different Collections, use the Object Browser explained in Step 3 to prepare a batch update file.

Instructions to obtain the update file:

Select the upper Inventory tab.
Navigate to FB Inventory → X.1 Materials → SAMPLES_SYNTHESIS → Samples.
Select the Sample objects that you want to connect.
Export the selected object metadata to an Excel file.
Save an unchanged backup copy of the exported file before editing it.

Instructions to prepare and upload the batch update:

Open the exported Excel file.
Identify the columns representing parent and child relationships.
Add the object identifiers required to connect samples from the same collection.
Edit only the relationship values that need to change. In this step, update Synthesized Material, Material Sample 001, and Material Sample 002.
Do not modify object identifiers, codes, column headings, or the worksheet structure.
Save the updated Excel file under a clear filename, for example samples_material_synthesis_connections.xlsx.
Return to the Samples Collection and select More → XLS Batch Update Objects.
Upload the updated file, verify the filename, and click Accept.
Open one of the updated Sample objects and verify their parent-child relationships.

Batch registration versus batch update: do not use XLS Batch Register Objects for this step. These Sample objects already exist. Batch registration creates new objects; batch update modifies existing objects.

Navigate to Samples collection — In Inventory, navigate to the **X.1 Materials** -> **Samples Synthesis** -> **Samples** collection and click on it to display registered **Samples**.

Display registered samples — Increase the **Rows per page** to see all samples registered by your colleagues.

Filter samples by co-responsible person — Use the **FILTERS** tab to **Filter Per Column**. Navigate to the **Co-responsible person** column and start typing your **user name** to select your samples.

Select samples to batch update and export excel file — Select the sample you want to update and export the Excel file. Samples to update are:**Synthesized Material**, **Material Sample 001** and **Material Sample 002**

Update excel file to set parent-child relationships — Update Excel file for $, **Parents** and **Children** columns using the sample **Identifier** to define the relationships and save the file.

Download example updated samples.xlsx

Batch update the samples — Navigate to **X.1 Materials → SAMPLES_SYNTHESIS → Samples**. Open the **More** drop-down menu and choose **XLS Batch Update Objects**.

Update Excel file to update the samples — Click **Datei auswählen/choose file**, select the updated Excel file **updated_samples.xlsx**, replace the file by your own and click **Accept**.

Verify the batch update

Visualise the connections you have created between the samples.

Navigate to updated samples — Navigate to the updated samples and visualize the connections.

Display Hierarchy Graph for updated samples — Open the Hierarchy Graph for the **Synthesized Material** sample that you registered to view the relationships.

hierarchical Synthesized Material — The Hierarchy Graph for the **Synthesized Material** sample that you registered should display by now all the connections you define in Steps 1 and 2. Click on the **Synthesized Material** sample, open the **More** menu and select **Hierarchy Graph**.

Step 3: Batch-update objects from different Collections

Identify the Objects to connect

In this step you will connect several samples with Experimental steps, instruments and Chemicals. The parent and child relationships must reflect the research workflow represented for Material Synthesis, the Instrument and Chemicals used by the activity are parents, while the Sample generated by the activity is a child when output or a parent when input to another Experimental Step.

Identify the remaining Objects and relationships that must be added to complete the workflow. Use the red-square workflow figure as the overview, then inspect the detailed relationship tables before collecting identifiers and preparing the cross-Collection update.

Relationships to add to the experimental step "Macrostructure characterization"

Relationship	Object type	Object Name	Role in the workflow
Parent	Sample	Material Sample 001	Sample used for the Experimental Step
Parent	Instrument	Macrostructure	Instrument used during the Experimental Step

Relationships to add to the experimental step "Chemical Treatment"

Relationship	Object type	Object Name	Role in the workflow
Parent	Sample	Material Sample 002	Sample used for the Experimental Step
Parent	Chemical	Treatment Solution	Chemical used during the Experimental Step
Child	Sample	Treatment Sample 001	Sample generated during the Experimental Step
Child	Sample	Treatment Sample 002	Sample generated during the Experimental Step

Relationships to add to the experimental step "Macrostructure characterization TS"

Relationship	Object type	Object Name	Role in the workflow
Parent	Sample	Treated Sample 001	Sample used for the Experimental Step
Parent	Instrument	Macrostructure	Instrument used during the Experimental Step

Relationships to add to the experimental step "Microstructure characterization"

Relationship	Object type	Object Name	Role in the workflow
Parent	Sample	Treated Sample 002	Sample used for the Experimental Step
Child	Experimental Step	Microstructure Data Analysis	Follow-up Experimental Step
Parent	Instrument	Microstructure	Instrument used during the Experimental Step

The complete “Material Synthesis” example is designed to connect several Collections and Object types. openBIS 20.10.12+ supports updating existing Objects of different types in different Collections from Tools → Utilities → Object Browser → XLS Batch Update Objects. In this tutorial, use this function to complete parent-child relationships in one Excel-based update.

What openBIS needs for a cross-Collection XLS batch update:

After you select the Object types, openBIS generates an Excel template. For every Object to be updated, the file must contain the unique Identifier. The Identifier is essential because it tells openBIS exactly which existing Object has to be updated.

Localize identifiers of objects to connect and export reference Excel files

The easiest and safest approach is to first collect the identifiers from the Collections where the Objects are already registered. Do not try to reconstruct identifiers from Object names.

Recommended way to collect identifiers:

Open the Collection that contains the Objects you want to update, for example Instruments, Chemicals, Samples, or a Lab Notebook Collection containing Experimental Steps.
In the Collection table, use Columns to display at least Identifier and Name. For Samples, also display Co-responsible person so that you can distinguish the Samples you registered from Samples with the same names registered by other members of your division.
If necessary, filter the table so that only the Objects needed for the Material Synthesis workflow remain.
Export the table with Import Compatible = Yes and export the selected columns and rows. Keep these exports as reference files; do not upload them as the cross-Collection update file.
Repeat this for each relevant Collection. You now have the exact identifiers of the existing Objects that you want to update to add relationships.

Why use Collection exports as reference files? The openBIS documentation explicitly describes an import-compatible table export as the preparation method for XLS batch updates within one Collection. For an update across several Collections, the documentation instead requires the template generated in Object Browser. Combining the two workflows is practical: use Collection exports to obtain reliable identifiers and use the Object Browser template as the file that you actually complete and upload.

Collections of objects to connect

Object type	Collection path	Objects
Sample	FB Inventory → X.1 Materials → SAMPLES_SYNTHESIS → Samples	Material Sample 001 Material Sample 002 Treated Sample 001 Treated Sample 002
Experimental Step	Lab Notebook → Home Space → Material Synthesis → Treatment non-destructive Lab Notebook → Home Space → Material Synthesis → Parameter 1 Lab Notebook → Home Space → Material Synthesis → Parameter 1 Lab Notebook → Home Space → Material Synthesis → Parameter 2 Lab Notebook → Home Space → Material Synthesis → Parameter 2 Analysis	Chemical Treatment Macrostructure Characterization Macrostructure Characterization TS Microstructure Characterization Microstructure Data Analysis
Instrument	BAM Inventory → BAM Equipment → X.1 Equipment Open → Instruments	Macrostructure Microstructure
Chemical	FB Inventory → X.1 Materials → CHEMICALS_SYNTHESIS → Chemicals	Treatment Solution

Example Excel file for Samples for batch updates — Confirm your name in **Co-responsible person** column for exported samples. You will need the **Identifier** to update **parents** and **child** relationships in the next step.

Navigate to Chemicals collection to filter columns — To collect identifiers of Chemicals to update, navigate in Inventory to the **Chemicals** collection and click on it to display registered **Chemicals** and click on the **COLUMNS** button.

Filter columns in Chemicals collection — Hide unnecessary columns by clicking **HIDE ALL** and select **name** and **Identifier** for export.

Select chemicals to batch update and export excel file — Select the chemicals you want to update and export the Excel file. Select **EXPORTS** conditions to include only the **name** and **Identifier** columns.

Example Excel file for Chemicals for batch updates — The exported Excel file will contain the **name** and **Identifier** columns for the selected chemicals. You will need the **Identifier** to update **parents** and **child** relationships in the next step.

Navigate to Instruments collection and export Excel file with name and identifier for Batch updates — In Inventory, navigate to the **Instruments** collection and click on it to display registered **Instruments**. Select the instruments you want to update and export the Excel file. The exported Excel file will contain the **name** and **Identifier** columns for the selected instruments. You will need the **Identifier** to update **parents** and **child** relationships in the next step.

In the Lab Notebook navigate to each collection of Experimental steps and export the Excel file with name and identifier for Batch updates — In the Lab Notebook, navigate to each Collection of Experimental steps and export the Excel file with name and identifier for Batch updates.

Update template for batch update Objects across collections with objects identifiers to define parent and child relationships

Before editing the template: Compare the Objects and relationships listed above with the Material Synthesis workflow. The batch update should complete the relationships that have not already been created in Steps 1 and 2.

Instructions:

Open Tools → Utilities → Object Browser.
Open the drop-down menu More and select XLS Batch Update Objects.
Select the Object types required for this update: Chemical, Instrument, Experimental Step, and Sample.
Download the Excel template generated by openBIS for these Object types.
Open the reference exports that you previously downloaded for Samples, Experimental Steps, Chemicals, and Instruments.
Open the Material Synthesis Data Model to visualize the relationships.
Use the Material Synthesis workflow as your reference. Complete the Sample relationships first, followed by the Experimental Step relationships, copying the required Object identifiers from your reference exports.
Review the identifiers and save the Excel file under a clear name, for example material_synthesis_relationships_batch_update.xlsx for batch update.
Return to Object Browser → XLS Batch Update Objects, upload the completed file, verify the filename, and click Accept.
Follow this tutorial step 4 to Visualise and verify relationship hierarchy.

Do not use the batch-registration workflow: these Objects already exist. Step 3 changes their relationships, so use XLS Batch Update Objects. Also keep an unchanged copy of each metadata export and of the completed update file before upload.

Important when editing an update file: the openBIS documentation states that removing a column or leaving a cell empty preserves the corresponding existing value. Deleting an existing value or parent-child connection requires the special deletion value defined by openBIS; do not use an empty cell to mean “delete”.

Open Object Browser — From **Tools → Utilities**, open the **XLS Batch Update Objects** function.

Suggested screenshot for Step 3 — Select object types to update:**Chemical, Instrument, Experimental Step, and Sample** and **Download** the Excel template for Batch update of correspondent objects.

Downloaded Excel template for batch update — The exported Excel file contains a sheet for each Object type previously selected.

Update objects of Samples — Update first **Samples**. Copy the **Name** for guidance and the **Identifier** of each Sample to update. Add the **Identifier** of the **Parent** and **Child** objects in correspondent columns.

Update objects of Experimental Steps — Update the **Experimental Steps**. Copy the **Name** for guidance and the **Identifier** of each Experimental Step to update. Add the **Identifier** of the **Parent** and **Child** objects in correspondent columns.

About the example Excel file: In the downloadable example, the worksheets for the Object types INSTRUMENT and CHEMICAL are intentionally left empty. The relationships involving these Object types are added to the corresponding SAMPLE and EXPERIMENTAL STEP Objects in their respective worksheets. The Instrument and Chemical identifiers are therefore referenced from those sheets rather than updated in separate INSTRUMENT or CHEMICAL rows.

Do not upload the example Excel file to openBIS. Use it only as a reference for how the parent-child relationships are represented. Complete the Excel template that you downloaded from openBIS with the identifiers of the Objects that you registered yourself in your Lab Notebook and in the corresponding Inventories of your division, and upload that completed file for your batch update.

Download example updated parent-child relationships.xlsx

Verify the cross-Collection update

Confirmation of batch update — openBIS displays a confirmation with the number of updated Objects.

Step 4: Visualise and verify the relationship hierarchy

After the relationships have been added, use openBIS to visualise the parent-child genealogy of an Object. The Hierarchy Graph displays Object-to-Object parent-child relationships; it does not display datasets.

Traceability through connected objects

The value of these connections becomes clear when researchers need to reconstruct what happened to a Sample or understand how a dataset was generated. The following use cases show how visualisation of parent-child relationships supports traceability in practice.

Parent Objects
Which resources or inputs led into this activity?

↓

Experimental Step
Which activity is documented here?

↓

Child Objects
Which Samples or downstream activities resulted from it?

Instructions to open the Hierarchy Graph of any object:

Navigate to the object and click on it to open the object form
In the Object form, open the More drop-down menu.
Select Hierarchy Graph.
Review the parents and children shown around the object.
If the graph is large, reduce with the slide bars for parents and children or reduce the number of Object types shown.

Use case 1: Imagine that several division members work in the same research project and registered Samples with the same descriptive name, Synthesized Material that contain additional metadata for their distinction. A researcher wants to track the provenance of a sample and answer practical questions such as: What was done with a Sample, and who generated it? Which experiment generated it? Which resources were used? Was the Sample used again later, and in which activity?

Select Sample — Navigate to the **Treated Sample 002** to open its object form.

Open the Hierarchy Graph — In the object form, open the **More** drop-down menu and select **Hierarchy Graph**.

Hierarchy Graph — The hierarchy graph with **Treated Sample_002** as starting node displays all related objects required to understand the provenance of the Sample.

What the hierarchy view contains: the relationship visualisation is an Object genealogy. The sample itself is the starting node (level 0 in green) of the Hierarchy Graph. To trace a sample, first open its object form from the collection, and visualise the sample's parent-child relationships.

Use case 2: Imagine a researcher finds a dataset in the Lab Notebook and wants to understand how it was generated and answer practical questions such as: What was done to generate this dataset? Which experiment generated it? Which resources were used? Can the process be reproduced?

What the hierarchy view contains: The dataset itself is not the starting node of the Hierarchy Graph. To trace a dataset, first open the Experimental Step to which the dataset is attached, and then visualise that Experimental Step's parent-child relationships.

Alternative view: Hierarchy Table

If a graphical tree is difficult to review, return to the Object form and select More → Hierarchy Table. This presents the genealogy of the selected Object in a tabular format and provides an alternative way to inspect the same parent-child relationships.

Use case 3: Explore the complete Material Synthesis workflow

Use case 3: Imagine a researcher wants to explore the activities related to the Material Synthesis research project and understand which experiments generated the Samples and which resources were used. Start from the Material Synthesis Experimental Step and use the Hierarchy Graph to explore the workflow visually. If the graph becomes too large or connected Objects are difficult to inspect, use the Hierarchy Table to review the same genealogy in tabular form.

Select Hierarchy level Experimental Step — Navigate to the experimental step **Material Synthesis** to open its form.

Open the Experimental Step form — In the object form, open the More drop-down menu and select **Hierarchy Graph** or **Hierarchy Table**.

What the hierarchy view contains: All activities related to the research project Material synthesis are displayed, their inputs and outputs, and the parent-child relationships between them. Note that not all instruments and chemicals are displayed for downstream nodes due to the size of the graph. An alternative to see all related objects is to select different nodes and open the Hierarchy Table.

Hierarchy table — The hierarchy table displays the parent-child relationships in a tabular format. Manage the displayed columns and rows by increasing the **Rows per page** and filter the table with the **COLUMNS** and **FILTERS** tabs.

Result

After completing this tutorial, you have connected the Objects of the Material Synthesis research workflow using parent-child relationships. You have:

connected an Experimental Step manually with its related Instrument, Chemicals, and generated Sample;
batch-updated parent-child relationships between Samples in the same Collection;
batch-updated parent-child relationships between Objects located in different Collections using the Object Browser;
completed the parent-child relationship network representing the Material Synthesis workflow; and
used the Hierarchy Graph and Hierarchy Table to verify the connections and trace the provenance of Samples and datasets.

These connections provide the context around the research data: datasets remain attached to the Experimental Steps that generated them, while parent-child relationships connect those Experimental Steps with the Samples, Instruments, Chemicals, and other Experimental Steps involved in the research workflow. Together, these linked Objects provide a traceable representation of the research workflow in the Data Store.

Connect Lab Notebook data with Inventory items

What you will learn

Before you begin

Tutorial sequence

Key concepts

Parent-child relationships

Parent-child hierarchy graph generated in openBIS

Traceability through connected objects

Use case 1: What was done with a Sample, and who generated it?

Use case 2: How was this dataset generated, and can the process be reproduced?

Connections for “Material Synthesis”

Tutorial workflow

Step 1: Connect one Experimental Step

Identify the Objects to connect

Relationships to add to the Experimental step “Material Synthesis”

Option 1: You know the Object name

Option 2: Find the Code to identify the object to connect

Add all parents and children to the Experimental Step

Register the connections

Step 2: Batch-update Samples from the same Collection

Identify the Objects to connect

Relationships to add to the sample "Synthesized Material"

Verify the batch update

Step 3: Batch-update objects from different Collections

Identify the Objects to connect

Relationships to add to the experimental step "Macrostructure characterization"

Relationships to add to the experimental step "Chemical Treatment"

Relationships to add to the experimental step "Macrostructure characterization TS"

Relationships to add to the experimental step "Microstructure characterization"

Localize identifiers of objects to connect and export reference Excel files

Collections of objects to connect

Update template for batch update Objects across collections with objects identifiers to define parent and child relationships

Verify the cross-Collection update

Step 4: Visualise and verify the relationship hierarchy

Traceability through connected objects

Alternative view: Hierarchy Table

Use case 3: Explore the complete Material Synthesis workflow

Result