Overview

BioNetDB models biology data as a network of nodes and relations.Biology data comes from different formats and sources it comprises  system biology data from Reactome, annotation data from CellBase and human genetic variations from healthcare centers' clinical data. BioNetDB relies on Neo4j graph database that allows users to access biological data using the Cypher query language (similar to SQL in relational databases). Neo4j is highly optimized for queries and it is scalable and reliable.

Modelling

Genes

Transcripts

Transcript node properties are:

• id

• name

• biotype

• chromosome

• start
• end
• strand

• proteinId

• genomicCodingEnd

• genomicCodingStart

• annotationFlags

• cdnaCodingEnd

• cdnaCodingStart

• cdsLength

• description

• status

Image below shows the transcript relationships:

Proteins

Protein Complex

Variants

Regulation

Pathway