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:
| Code Block | ||
|---|---|---|
| ||
./bionetdb.sh import -i <input-directory> -o <output-csv-directory> --create-csv-files |
- Load the create Neo4j CSV files into the database:
| Code Block | ||
|---|---|---|
| ||
./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:
| Code Block | ||
|---|---|---|
| ||
match (n:TRANSCRIPT) return n.id, n.name, n.biotype, n.chromosome, n.start, n.end, n.annotationFlags limit 10 |
| n.id | n.name | n.biotype | n.chromosome | n.start | n.end | n.annotationFlags |
|---|---|---|---|---|---|---|
| "ENST00000553557" | "TSPYL2-003" | "retained_intron" | "X" | "53111549" | "53115595" | "-" |
| "ENST00000375442" | "TSPYL2-001" | "protein_coding" | "X" | "53111549" | "53117722" | "CCDS;basic" |
| "ENST00000579390" | "TSPYL2-005" | "protein_coding" | "X" | "53111563" | "53115300" | "mRNA_end_NF;cds_end_NF" |
| "ENST00000578306" | "TSPYL2-006" | "nonsense_mediated_decay" | "X" | "53112175" | "53115021" | "cds_start_NF;mRNA_start_NF" |
| "ENST00000556808" | "TSPYL2-004" | "retained_intron" | "X" | "53112305" | "53117721" | "-" |
| "ENST00000463525" | "TSPYL2-002" | "retained_intron" | "X" | "53113881" | "53115125" | "-" |
| "ENST00000314888" | "TLN1-001" | "protein_coding" | "9" | "35696945" | "35732392" | "CCDS;basic" |
| "ENST00000540444" | "TLN1-201" | "protein_coding" | "9" | "35697334" | "35732392" | "basic" |
| "ENST00000489255" | "TLN1-003" | "processed_transcript" | "9" | "35698041" | "35699325" | "-" |
| "ENST00000464379" | "TLN1-005" | "processed_transcript" | "9" | "35703556" | "35707871" | "-" |
| Code Block | ||
|---|---|---|
| ||
match (n:VARIANT) return count(n) |
| count(n) |
|---|
| 9010279 |
Table of Contents:
| Table of Contents | ||
|---|---|---|
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