🧭Configure your Knowledge Graph Schema

The foundry is where you customize and manage your knowledge graph schema. The foundry can be accessed using the top application toolbar.

Overview

The overview is where you will see live metrics from your knowledge graph and a diagram of your graph schema.

A quick action panel can be accessed on the right to manage your graph schema and data.

External Data Packages

By default the knowledge graph is completely blank. To quickly get started you can load in an external data package. An external data pack is a set of standardized concepts, relationships and/ or objects preconfigured by the BioBox team. This data is derived from industry standard knowledge bases and consortiums such as OpenTargets, Reactome, UBERONon and more. Each data pack is versioned, accompanied by documentation and updated on a monthly basis.

To browse the available data packages, select the "External data package" tab. Here you will see a list of all preconfigured data packages.

Importing Data Packs

To import a package, select the import button in the top right hand corner of the card. When you import a data package, all of the concepts and relationships listed in the preview card will automatically be added to your knowledge graph schema.

Data Pack Dependencies

Some data packages have dependencies for concepts such as Genes and Diseases. This would require those concepts to be available in your knowledge graph prior to the import of the data package. When you hover over the import button you will be notified of any dependencies that need to be imported first.

Concepts

The concepts tab displays all of the concepts within your graph and their hierarchy that were created by you or imported through a data pack. Think of concepts as overarching categories such as Drugs, Diseases and Pathways.

Selecting a concept will display all of the information and data objects associated with the concept.

Creating New Concepts

Select "Create New Concept" provide a name and a description. If the concept is a subclass of another concept you can specify its parent concept.

Editing Concepts

To edit the name and description of the concept select the edit icon next to each

To update the relationships and data properties associated with a concept select "view in database" and this will open the administrative panel.

Deleting Concepts - Deletion Impact Analysis

To delete a concept select the trash icon located in the top right hand corner of the concept. This will open an impact analysis that will show you all of the downstream impacts that will occur if you delete the concept.

Properties

The properties tab displays all of the data properties within your knowledge graph.

Relationships

The relationships tab displays all of the relationships within your graph that were created in your organization or were imported though a data pack.

Creating New Relationships

Select "Create Relationship" and specify the name, description domain (concepts this relationship points from) and range (concepts this relationship points to).

Editing Relationships

Select "Edit Properties" and you will be able to add data properties to the relationship.

Deleting Relationships - Delete Impact Analysis

To delete a relationship select the trash icon located in the top right hand corner. This will open the delete impact analysis, showing you the downstream impacts that will occur when the relationship is deleted. This will remove the relationship but will preserve the concepts that the relationship points to and from.

Data Upload

The Data Upload tab is where you can upload your internal data formatted as a data package. A detailed explanation can be found here.