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
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

.. code-block:: xml

    <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

.. code-block:: xml

	<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:

.. code-block:: properties

       <TAXON_ID>.<GENE_IDENTIFIER_FIELD>=shortLabel

`xref`

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

.. code-block:: properties

	<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.

.. index:: BioGRID