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.