:orphan:

Data files to integrate
===========================

All data required to build an InterMine is included in `biotestmine/data/malaria-data.tar.gz <https://github.com/intermine/biotestmine/tree/master/data/malaria-data.tar.gz>`_. Copy this file to your local directory and extract from the archive.

.. code-block:: bash

	cp biotestmine/data/malaria-data.tar.gz DATA_DIR
	cd DATA_DIR
	tar -zxvf malaria-data.tar.gz

Edit the project.xml file so that all occurrences of ''DATA_DIR'' point to the your local data directory location. 

Data sources
-----------------

malaria-genome
~~~~~~~~~~~~~~~~~~

The malaria genome as gff3 and fasta, originally downloaded from PlasmoDB

uniprot
""""""""""""""""

UniProt XML with protein information and sequences from SwissProt and Trembl. Downloaded from uniprot.org and filtered on taxon id 36329.

gene_ontology
~~~~~~~~~~~~~~~~~~

The Gene Ontology structure. Downloaded from http://www.geneontology.org/

go_annotation
~~~~~~~~~~~~~~~~~~

GO term assignments for *P. falciparum*.  Downloaded from http://www.geneontology.org/