Ensembl Core

This page describes how to load Ensembl core data into your InterMine-bio database.

Generate Items XML file

Ensembl Data

First you will need the data from Ensembl, which are available via MySQL databases. Download the Ensembl MySQL database and create the database locally:

ftp://ftp.ensembl.org/pub/current_mysql

for example: download homo_sapiens_core_70_37 to a local directory, unzip all gz files, and load it to your MySQL database

# create a new db in MySQL
$ mysql -u DB_USER -p
mysql> create database homo_sapiens_core_70;

# load data into db
$ mysql -u DB_USER -p homo_sapiens_core_70 < homo_sapiens_core_70_37.sql
$ mysqlimport -u DB_USER -p homo_sapiens_core_70 -L *.txt -v

Update <MINE_NAME>.properties

Add the location of the downloaded Ensembl MySQL databases to your mine properties file, for example:

# core database
db.ensembl.9606.core.datasource.serverName=SERVER_NAME
# port: uncomment the next line if use different port other than 3306
# db.ensembl.9606.core.datasource.port=PORT_NUMBER
db.ensembl.9606.core.datasource.databaseName=homo_sapiens_core_70
db.ensembl.9606.core.datasource.species=homo_sapiens
db.ensembl.9606.core.datasource.user=DB_USER
db.ensembl.9606.core.datasource.password=DB_PASSWORD

These properties are used by the Perl script.

Install Perl modules

Ensembl

InterMine’s Ensembl converter uses Ensembl’s Perl API. Follow Ensembl’s instructions for how to install the necessary Perl modules:

http://www.ensembl.org/info/docs/api/api_installation.html

InterMine

You will also need to install InterMine’s Perl modules, see Perl

Run Script to Generate Items XML

Run this command in /bio/scripts

$ ./ensembl.pl [Release Version] MINE_NAME TAXONID DATA_DESTINATION

for example:

$ ./ensembl.pl flymine 7165 /data/ensembl/current

Load XML file into InterMine database

Add Ensembl core to the list of datasources to be integrated

This is located in the project.xml file, and it should look something like:

<source name="ensembl" type="ensembl-core">
 <property name="src.data.dir" location="/MY_DATA_DIR/ensembl"/>
</source>

When you run a database build, every XML file in the directory specificed will be processed and loaded into the database.

Run InterMine build

Run a build. The entry in project.xml will instruct the build process to load the XML files you created in the previous step into the database. For example, run this command in MINE_NAME/integrate:

$ ant -v -Dsource=ensembl