🧭Configure your Knowledge Graph Schema
How to customize your knowledge graph schema
The foundry is where you customize and manage your knowledge graph schema. The foundry is the home page of the application and can be accessed at any time using the top application toolbar.
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.
Overview
The overview is where you will see a schematic diagram of all of the concepts and relationships within your graph.
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.
Creating New Concepts
To create a concept you will have to provide a label (Name) and a description. If the concept is a subclass of another concept you can specify its parent concept.
Selecting a concept will open the side panel where you can see the information associated with each concept
Editing Concepts
To edit the concept and see the associated objects, select the open button located in the top right hand corner of the information panel.
Deleting Concepts
To delete a concept select the trash icon located in the top right hand corner. This will remove the concept but will preserve the underlying objects within your graph
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 by you or were imported though a data pack.
Creating New Relationships
Select "+ 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
To delete a relationship select the trash icon located in the top right hand corner. 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.
When uploading your data, the concepts and relationships that the data relates to must be created first. Please follow the instructions in this article to set up your graph schema prior to uploading proprietary data.
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