BioNetDB
Page tree
Skip to end of metadata
Go to start of metadata

You are viewing an old version of this page. View the current version.

Compare with Current View Page History

« Previous Version 4 Next »

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:

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


  • Load the create Neo4j CSV files into the database:

Load CSV files
./bionetdb.sh import -i <csv-directory>



Table of Contents:


  • No labels