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  • How To
    • 🧭Configure your Knowledge Graph Schema
      • πŸ—‚οΈFormat Internal Data For Uploading
      • ‴️Upload Internal Data
    • βš–οΈCreate Prioritization Graph Models
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      • βš™οΈRunning Graph Algorithms
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    • πŸ”—Use the Query Language
      • Customize the data table returned with your query
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      • πŸ“ŠVisualize data returned in Query Language
      • ✏️Modify Queries using the Query Editor
    • Ask questions with Natural Language (GraphRAG)
      • Use Agent Orion to generate a query with Natural Language
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  • πŸ“ŠVisualize data on the Legacy Platform
    • πŸ“„Create a Genomic Sequencing Dashboard (Legacy Platform)
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    • ↕️Upload raw data (Legacy Platform)
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  • External Data Packages
  • Overview
  • Concepts
  • Properties
  • Relationships
  • Data Upload
  1. How To

Configure your Knowledge Graph Schema

How to customize your knowledge graph schema

PreviousPhenotypeNextFormat Internal Data For Uploading

Last updated 11 months ago

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, 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

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.


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

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can be found here
accompanied by documentation
Foundry External Data Packages
Foundry Overview
Foundry Concepts