BioGRID

Loads interactions data from BioGRID

Types of data loaded

genes, proteins, interactions

How to download the data

From the download section of the BioGRID website: http://thebiogrid.org

Download the file named: BIOGRID-ORGANISM-[version].psi25.zip.

How to load the data into your mine

Project XML example

<source name="biogrid" type="biogrid">

<property name="src.data.dir" location="/DATA/biogrid"/>

<property name="src.data.dir.includes" value="*psi25.xml"/>

<property name="biogrid.organisms" value="7227 6239 4932"/>

</source>

biogrid_config.properties

Determines which gene identifiers are set. organisms - If none are configured, all interactions are stored.

This is what the gene looks like in biogrid

<names>

<shortLabel>CG1111</shortLabel>

</names>

<xref>

<primaryRef db="FLYBASE" id="FBgn001" />

shortLabel

To set your gene.identifier to be the shortLabel in the biogrid XML, use this config:

<TAXON_ID>.<GENE_IDENTIFIER_FIELD>=shortLabel

xref

To set your gene.identifier field to be a value from an xref entry, use this syntax:

<TAXON_ID>.xref.<GENE_IDENTIFIER_FIELD> = <XREF_DB_VALUE>

Note xref "db" value is not case sensitive, case seems to vary from file to file.