reactome-orientdb

Introduction

Hello and welcome to the reactome-orientdb repository!

The aim of this repository is to make the Reactome database available as a graph in OrientDB, the Graph/Document Multi-Model Database.

We have imported the Reactome graph database into OrientDB using the Neo4j to OrientDB Importer, and then optimized the Reactome structure for OrientDB.

The reactome database is updated every 3-4 months. To start with, please select the branch related to your Reactome version (e.g. 59, 61): from there you will be able to download the migrated database directly.

Note: not all versions may have been imported into OrientDB - but you can perform the migration yourself, if needed (see below).

Please open an issue if you have any questions or problems.

Many thanks,

Using a migrated version

To use a version of the Reactome database that has been migrated already to OrientDB:

• Download the reactome.zip archive from one of the branches of this repository (identify the one corresponding to your database version, if it exists)
• Unzip reactome.zip into the databases directory of your OrientDB installation

High-level migration steps

Step 1: Download the Neo4j version of Reactome

Step 2: Download and install OrientDB and the Neo4j to OrientDB Importer, e.g.

$ wget http://mkt.orientdb.com/CE-2216-multiOS -O orientdb-community-2.2.16.zip
$ unzip orientdb-community-2.2.16

$ wget http://mkt.orientdb.com/importer-2216-tar -O orientdb-neo4j-importer-2.2.16.tar.gz
$ tar xfv orientdb-neo4j-importer-2.2.16.tar.gz -C orientdb-community-2.2.16 --strip-components=1

Step 3: Migrate the database from Neo4j to OrientDB with a command similar to the following:

$ ./orientdb-neo4j-importer.sh \
    -neo4jlibdir /home/santo/neo4j/neo4j-community-3.0.7/lib \          
    -neo4jdbdir /home/santo/neo4j/data/reactome.graphdb \
    -odbdir /home/santo/orientdb/orientdb-community-2.2.16/databases/reactome \    

Step 4: Optimize the structure of the Reactome database in OrientDB by applying the list of SQL statements included in the file optimize_reactome_orientdb.osql, e.g. using the OrientDB console:

$ ./console.sh optimize_reactome_orientdb.osql

Note: if you are using OrientDB 2.2.16 or below, before executing the above command please open console.sh and change the value of the -Xmx512m parameter to -Xmx1024m. Starting with OrientDB 2.2.17 we have raised this by default, so this step won't be necessary.

Step 5: Start an OrientDB server:

$ ./server.sh

Step 6: Point your browser to http://localhost:2480 and connect to the reactome database using user admin and password admin.

Querying the Reactome DB

Some query examples are reported below (please execute them from the "Graph Editor" Tab).

Retrieving objects based on their identifier

Example #1

MATCH {class: vpathway, as: pathway, where: (stId = 'R-HSA-1236975')}
RETURN $pathelements

Example #2

MATCH {class: vEntityWithAccessionedSequence, as: ewas, where: (stId = 'R-HSA-199420')}
RETURN $pathelements

Querying vertices connected by specific edges types

Example #1

MATCH {class: vEntityWithAccessionedSequence, as: ewas, where: (stId = 'R-HSA-199420')}-referenceEntity->{class: vReferenceEntity, as: re}
RETURN $pathelements

Example #2

MATCH {
	   class: vEntityWithAccessionedSequence, as: ewas, where: (stId = 'R-HSA-199420')
	  }-referenceEntity->{
	   class: vReferenceEntity, as: re
	  }-referenceDatabase->{
	   class: vReferenceDatabase, as: rd}
RETURN $pathelements