BioNetDB
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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.

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Modelling

Genes


The figure below shows BioNetDB nodes with their labels. for clarity, some labels have been shortened:


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Shortened labes in the previous figure:

Shortened labelNode label

1 POPUL. FREQUEN

POPULATION_FREQUENCY
2 FUNCT. SCOREFUNCTIONAL_SCORE

3 TRAIT ASSOCIA.

TRAIT_ASSOCIATION

4 CONSEQ. TYPE

CONSEQUENCE_TYPE
5 PROTEIN VAR. ANNOT.PROTEIN_VARIANT_ANNOTATION
6 SUBST. SCORESUBSTITUTION_SCORE
7 KEYWORDPROTEIN_KEYWORD
8 FEATUREPROTEIN_FEATURE


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:

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Transcripts

Transcript node properties are:

  • uid

  • id

  • name

  • biotype

  • chromosome

  • start
  • end
  • strand

  • proteinId

  • genomicCodingEnd

  • genomicCodingStart

  • annotationFlags

  • cdnaCodingEnd

  • cdnaCodingStart

  • cdsLength

  • description

  • status

Image below shows the transcript relationshipsTranscript relationships (transcript node in pink):

Proteins

Protein

Complex

Variants

Regulation

Pathway

node properties:

  • uid

  • id

  • name

  • accession

  • dataset

  • evidence
  • proteinExistence

Protein relationships:

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Protein complex

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Variants

Variant node properties:

  • uid

  • id

  • name
  • chromosome
  • start
  • end
  • strand
  • type
  • alternate
  • reference

  • alternativeNames

Variant relationships:

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Regulation

Regulation node properties:

  • uid

  • id

  • name

Regulation relationships:

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Pathway

Pathway node properties:

  • uid

  • id

  • name

Pathway relationships (pathway nodes in yellow):

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Table of Contents:

Table of Contents
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