Overview
BioNetDB models biology data as a network of nodes and relations.Biology data comes from different formats and sources it comprisesĀ 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 languageĀ (similar to SQL in relational databases). Neo4j is highly optimized for queries and it is scalable and reliable.
This section describes the main nodes of the BioNetDB network data model and for each node its properties and relationships are shown.
Gene node properties:
uid
id
name
chromosome
start
end
strand
description:
source
status
Gene relationships:
Transcript node properties:
uid
id
name
biotype
chromosome
proteinId
genomicCodingEnd
genomicCodingStart
annotationFlags
cdnaCodingEnd
cdnaCodingStart
cdsLength
description
status
Transcript relationships (transcript node in pink):
Protein node properties:
uid
id
name
accession
dataset
Protein relationships:
Variant node properties:
uid
id
alternativeNames
Variant relationships:
Regulation node properties:
uid
id
Regulation relationships:
Pathway node properties:
uid
id
Pathway relationships (pathway nodes in yellow):
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