Generator: The 3D Knowledge Graph

Open, navigate, and inspect the PrimeKG knowledge graph that powers every hypothesis.

Open the Knowledge Graph

The Generator is where every hypothesis begins. From the Hub, click "Start" on the Targets card. The Generator opens with a 3D knowledge graph powered by PrimeKG — 130,000 biomedical entities and 8 million curated relationships rendered as an interactive force layout you can rotate, zoom, and click into.

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Open the Knowledge Graph

Generator with 3D graph

From the Hub, click "Start" on the Targets card. The Generator opens with the 3D knowledge graph and the left sidebar in view.

Mouse controls:

  • Left-click drag — Rotate the graph
  • Scroll wheel — Zoom in/out
  • Click a node — Select it and view details
  • Right-click a node — Open the annotation menu (up-regulate / down-regulate)
  • Hover — See node name and type in a tooltip
Tip: If the graph feels disorienting at first, turn off Auto-rotate in the toolbar and use a fixed Viewpoint (Front / Top / Center) while you find your bearings.
Note: Loading a hypothesis and annotating regulation is covered in the Generator: Building a Hypothesis chapter. This chapter is about exploring the graph itself — the toolbar, the sidebar, the radiating layout, and node details.

Generator Toolbar Reference

The top toolbar in the Generator holds the controls for interacting with the graph and managing your workspace.

ButtonWhat It Does
Sidebar toggleShow or hide the left panel
Load Example(s)Open the Examples popup — load a pre-loaded bold hypothesis with disease + regulated targets in one click
Select Disease(s)Open disease selection — the graph radiates from your chosen disease (no pre-regulated nodes)
Select PathChoose specific pathways in the radiating layout
Layer count (1–2)How many hops outward from the disease to display
Viewpoint (Front / Top / Center)Switch the 3D camera angle
Auto-rotateToggle automatic camera rotation
Undo / RedoRevert or redo your last annotation
Saved SpacesLoad or create named hypothesis workspaces
WaitlistView all submitted hypotheses and their validation status

The left sidebar organizes everything around the active hypothesis. It has four tabs:

At the bottom of the sidebar you will also find Guide Me (opens this user guide), Feedback Screenshot, your user info, and Sign Out.

Tip: The Search tab is the fastest way to jump to a specific gene, protein, or drug in a dense graph — type the name, click the result, and the camera flies to that node.

Explore the Disease Neighborhood

Once a disease anchors the graph, the layout reorganizes into concentric rings so you can read the biology outward from the disease itself.

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Explore the disease neighborhood

Radiating layout

The radiating layout shows your disease at the center with associated genes, proteins, drugs, and pathways radiating outward in concentric layers. Each layer = one hop in the knowledge graph.

Tip: Use the Layer selector to toggle between 1 layer (direct neighbors only — a focused hypothesis) and 2 layers (one hop further — broader context). For deeper exploration, use Select Path to pick specific pathways.

View Node Details

Every node carries its own evidence dossier. Clicking a node opens a Details Modal whose contents adapt to the node type.

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View node details

Node details modal

Click any node to open its Details Modal. Content varies by node type:

  • Gene / Protein: UniProt function, amino acid sequence, ClinGen validation, COSMIC cancer data.
  • Drug: SMILES structure, mechanism of action, ChEMBL bioactivity, clinical stage, developability profile.
  • Disease: Related genes, approved drugs, clinical trial count.
  • Publication: Title, authors, journal, abstract, related entities.
Node TypeWhat the Details Modal Shows
Gene / ProteinUniProt function, amino acid sequence, ClinGen validation, COSMIC cancer data
DrugSMILES structure, mechanism of action, ChEMBL bioactivity, clinical stage, developability profile
DiseaseRelated genes, approved drugs, clinical trial count
PublicationTitle, authors, journal, abstract, related entities
Note: From a node's Details Modal you can right-click a target to annotate its regulation — the green / red pill workflow that turns exploration into a hypothesis. That step is documented in the Generator: Building a Hypothesis chapter.

BioinvestGPT BVCT Platform User Guide — Generator: The 3D Knowledge Graph. BVCT outputs are model-based decision-support analyses, not investment advice. Prospective track record: data.bioinvestgpt.com.