Projects

Organize your research into Projects - rich containers that capture context, hypotheses, and findings.

What are Projects?

Projects are research containers that go beyond simple collections. They let you:

• Group related Query Cards together
• Document your research hypothesis
• Add notes and observations
• Link external resources (papers, pathways)
• Collaborate with team members

Creating a Project

From Scratch

1. Go to Projects in the navigation
2. Click New Project
3. Enter a name and optional description
4. Add your hypothesis (optional but recommended)

From Query Results

After running a query:

1. Click Save to Project on the Query Card
2. Choose an existing project or create a new one
3. Optionally mark as a key finding

From an Exploration

If you’ve been running queries in an Exploration session:

1. Click Save as Project on the exploration page
2. All queries from the session are converted to project cards

Project Components

Cards

Query Cards saved to your project. Each card includes:

• Original query and results
• Position (drag to reorder)
• Section assignment (e.g., “Expression Analysis”, “Survival”)
• Key finding flag
• Personal notes

Hypothesis

Document your research hypothesis at the project level. This appears prominently and helps frame your investigation.

Example:

DDR1 overexpression in papillary RCC may serve as a prognostic biomarker and therapeutic target.

Notes

Add timestamped notes to document:

• Observations from your analysis
• Questions to explore
• Decisions made
• Meeting notes

Note types: note, observation, question, decision

External Links

Link related resources:

Collaboration

Sharing Projects

Projects can be shared with collaborators:

1. Go to your project
2. Click Invite Collaborators
3. Enter email addresses
4. Choose their role

Roles

Project Visibility

To share a project publicly, publish it as a Study.

Best Practices

Organizing by Investigation

Create projects around research questions, not just genes:

Good: “DDR1 as Therapeutic Target in RCC” Less Good: “DDR1 Queries”

Using Sections

Group cards into logical sections:

• Background - Initial expression/mutation checks
• Mechanism - Pathway and correlation analyses
• Clinical - Survival and subtype analyses
• Validation - Cross-dataset confirmation

Documenting as You Go

Add notes while your reasoning is fresh:

• Why did you run this query?
• What did you expect vs. find?
• What follow-up does this suggest?

Converting to Study

Ready to share your findings? Projects can be published as Studies:

1. Open your project
2. Click Publish as Study
3. Add title, summary, and key findings
4. Choose visibility
5. Share with the community

See Publishing Studies for details.