BioNetDB
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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

In order to populate BioNetDB database, you should import you data into the Neo4j database by using BioNetDB command line. Importing data consists of two steps:

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

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


  • Load CSV files into the database

Start Catalog Daemon
./bionetdb.sh import -i <csv-directory>



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