Explorations

Run multi-query analysis sessions with context tracking and intelligent suggestions.

What are Explorations?

Explorations are guided research sessions that:

• Track context across multiple queries
• Suggest relevant follow-up analyses
• Remember what you’ve discovered
• Can be converted to Projects or Studies

Starting an Exploration

1. Go to Explorations in the navigation
2. Click New Exploration
3. Ask your first question

BioQuery will automatically track context as you explore.

The Exploration Interface

Chat View

Explorations use a chat-like interface:

• Your queries appear on the right
• Results appear on the left with summaries
• Suggestions appear below as clickable chips

Context Panel

At the top, you’ll see tracked context:

• Genes: Gene symbols mentioned in your queries
• Cancers: Cancer types you’re investigating
• Current Focus: What BioQuery thinks you’re exploring

This context helps BioQuery understand follow-up questions.

Context-Aware Queries

With Context

Once context is established, you can ask abbreviated questions:

First query:

“Is DDR1 overexpressed in papillary kidney cancer?”

Follow-up (with context):

“What about survival impact?”

BioQuery understands you mean “Does DDR1 expression affect survival in KIRP?”

Resetting Context

To start fresh within the same exploration:

• Say “Looking at a different gene now…” before your query
• Or start a new exploration

Suggestions

After each result, BioQuery suggests relevant follow-ups.

Suggestion Types

Using Suggestions

• Click a suggestion to run that query
• Dismiss (X) suggestions you’re not interested in
• Ignore - suggestions will update after your next query

Example Exploration

Here’s a typical exploration session:

1. Start: “Is DDR1 higher in papillary vs clear cell kidney cancer?”

   • Result: Yes, significantly higher (p < 0.001)

2. Suggestion clicked: “Does DDR1 expression affect survival in KIRP?”

   • Result: High DDR1 associated with worse survival (p = 0.023)

3. Your follow-up: “Is it also elevated vs normal kidney?”

   • Result: Yes, 3.2x higher than GTEx normal kidney

4. Your query: “Is DDR1 mutated in kidney cancer?”

   • Result: Low mutation rate (2.3%)

This progression builds a complete picture of DDR1 in kidney cancer.

Managing Explorations

Naming

Explorations are auto-named based on context, or you can rename them.

Finding Past Explorations

Go to Explorations to see your history:

• Sorted by last activity
• Shows context summary (genes, cancers)
• Click to continue exploring

Deleting

You can delete explorations you no longer need from the list view.

Converting Explorations

To Project

Save your exploration as a Project to:

• Organize cards into sections
• Add hypothesis and notes
• Collaborate with others

Click Save as Project on any exploration.

To Study

Publish your exploration as a Study to:

• Share with the community
• Get feedback from experts
• Contribute to scientific discovery

Click Publish Study on any exploration.

Best Practices

Start Broad, Then Narrow

Begin with general questions, then drill down:

1. Is gene X altered in cancer Y?
2. Does it affect outcomes?
3. What’s the mechanism?

Use Suggestions as Guides

Suggestions represent common research patterns. Even if you don’t click them, they can inspire your next question.

Save Important Findings

When you find something interesting:

• Click “View full result” to see the complete Query Card
• Save to a Project for organization
• Add notes while the context is fresh

Convert Long Sessions

After 5+ queries, consider converting to a Project. This helps organize your findings and makes them easier to revisit.