Quick Start

This guide gets you running MCBO in minutes using the included demo data.

Prerequisites

Ensure you have completed the Installation steps:

conda activate mcbo
make install

Running the Demo

The fastest way to see MCBO in action:

make demo

This single command:

  1. Builds a graph from the demo studies in data.sample/studies/

  2. Runs all 8 competency question (CQ) SPARQL queries

  3. Displays statistics and results

Expected output:

Building demo graph...
Running CQ evaluation on demo data...

=== EVALUATION SUMMARY ===
Graph: data.sample/graph.ttl
Queries: eval/queries

CQ Results:
  cq1: 13 results
  cq2: 2 results
  cq3: 4 results
  ...

✅ Demo data processing complete

Understanding the Output

Demo Data Structure

data.sample/
├── studies/                  # Input: study directories
│   ├── study_demo_001/
│   │   ├── sample_metadata.csv
│   │   └── expression_matrix.csv
│   └── study_demo_002/
│       └── sample_metadata.csv
├── graph.ttl                 # Generated: evaluation graph
├── mcbo-instances.ttl        # Generated: instance data
└── results/                  # Generated: CQ results
    ├── cq1.tsv
    ├── cq2.tsv
    └── SUMMARY.txt

Generated Files

  • graph.ttl - The merged evaluation graph (TBox + ABox) used for SPARQL queries

  • mcbo-instances.ttl - Instance data (ABox) generated from CSV files

  • results/*.tsv - Tab-separated query results for each competency question

Manual Steps (Alternative)

If you prefer to run commands individually:

# Step 1: Build the graph
mcbo-build-graph build --data-dir data.sample

# Step 2: Run evaluation queries
mcbo-run-eval --data-dir data.sample

# Step 3: View statistics
mcbo-stats --data-dir data.sample

# Step 4: Check the results
cat data.sample/results/SUMMARY.txt

Running QC Checks

To validate the ontology with ROBOT:

make qc

This runs quality control queries that check for:

  • Orphan classes (classes without parents)

  • Duplicate labels

  • Missing definitions

Run Everything

To run the complete CI/CD pipeline locally:

make all    # Runs demo + qc

Or for a full CI check including verification:

make ci     # Runs install + qc + demo + verify-demo

Next Steps