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).
The figure below shows BioNetDB nodes with their labels. for clarity, that labels may be shortened:
Modelling
This section lists the main nodes of the BioNetDB network data model and for each of them, its properties and relationships are shown.
Genes
Gene node properties:
uid
id
name
chromosome
start
end
strand
biotype
description:
source
status
Gene relationships:
Transcripts
Transcript node properties:
uid
id
name
biotype
chromosome
start
end
strand
proteinId
genomicCodingEnd
genomicCodingStart
annotationFlags
cdnaCodingEnd
cdnaCodingStart
cdsLength
description
status
Transcript relationships (transcript node in pink):