Pre-requisites 

In order to follow this guide you have to install BioNetDB in your system. Please, please follow the steps on installation guide and set it up.

Download test data

Users can download test data from the following link. Download the tar.gz file and uncompress in your system. Once uncompressed, you should see the following files:

• genes.json.gz
• proteins.json.gz
• mirna.csv
• hsapiens.biopax.owl
• 1k.clinvar.json
• 5k.variants.json

Import genomic data

Before you query BioNetDB database, you have to populate it by importing your data into the Neo4j database. BioNetDB provides a command line interface to import data. First, you prepare your data, and then, you load into the BioNetDB database:

• Prepare your data, i.e., transform your genomic data files into Neo4j CSV files:
  
  

./bionetdb.sh import -i <input-directory> -o <output-csv-directory> --create-csv-files

• Load the create Neo4j CSV files into the database:
  
  

./bionetdb.sh import -i <csv-directory>

Accesing BioNetDB from Neo4j browser interface

Now you can access to your BioNetDB database from the Neo4j browser interface. Open the http://localhost:7474 from your internet browser:

And you can execute Cypher queries as shown below. For a Cypher tutorial, please refer to the Intro to Cypher from the Neo4j Team.

Some Cypher queries:

match (n:TRANSCRIPT) return n.id, n.name, n.biotype, n.chromosome, n.start, n.end, n.annotationFlags limit 10

match (n:VARIANT) return count(n)