NDEx Interactome Search service

Interactome search service for NDEx iQuery. This service has two components.

1. Interactome search: find subnetworks that relate to your query gene set from a collection of protein protein interaction networks.
2. Gene association search: find subnetworks that relate to your query gene set from a collection of gene association networks such as gene-chemical assocation networks and gene-disease association networks etc.

Build the service

Requirements:

• Java 11+ JDK
• Maven 3.6 or higher

Commands below build Interactome Service assuming machine has Git command line tools installed and above Java modules have been installed:

# In lieu of git one can just download repo and unzip it
git clone https://github.com/cytoscape/ndex-interactome-search.git

cd /ndex-interactome-search
mvn clean test install

The above command will create a jar file under target/ named interactomeSearch-.jar that is a command line application

Deloy, Configure and Running NDEx Interactome Search REST Service

Step 1 Deploy the service

For simplcity, we recommend deploying this service on the same server that your NDEx server is running on. If you want to scale up this service, you can also deploy this service to a seperate server, as long as the the file system of your NDEx server is mounted to that server. On the target server, create directory interactome and copy interactomeSearch-.jar into that directory.

# change to the interactome search directory
cd interactome

# create directory
mkdir logs 

Step 2 Build the index for Interactome Search

Create an configuration file. This configuration file is in JSON format and has two lists in it. Attribute associationNetworks contains a list of gene association networks that this service will search. Attribute ppiNetworks contains a list of protein-protein interaction networks that the service will search. The value of attribute UUID is the UUID of the network stored in your NDEx server. Here is an example of networks.json file:

cat networks.json
{
	"associationNetworks": [
		{"uuid":"109a36a9-a4d2-11e9-8818-525400c25d22"},
		{"uuid":"0e00c717-a4d2-11e9-8818-525400c25d22"},
		{"uuid":"0498a7f8-a756-11e9-8818-525400c25d22"},
		{"uuid":"92e74213-a4d1-11e9-8818-525400c25d22"},
		{"uuid":"8b1eeaf1-a4d1-11e9-8818-525400c25d22"}
	],
	"ppiNetworks": [
    {"uuid":"d5a8d887-a816-11e9-85eb-525400c25d22"},
		{"uuid":"3dcf562a-a80d-11e9-85eb-525400c25d22"},
		{"uuid":"f3015235-a80a-11e9-85eb-525400c25d22"},
		{"uuid":"aeb77786-a4d1-11e9-8818-525400c25d22"},
		{"uuid":"bc1ce496-1b82-11ea-a0f6-525400c25d22"}
	]
}

After creating the configuration file, build the index using this command

java -classpath interactomeSearch-<VERSION>.jar org.ndexbio.interactomesearch.GeneSymbolIndexer ./genedb /opt/ndex/data/ networks.json public.ndexbio.org

genedb is the name of the database you created for interactome search. /opt/ndex/data/ is the path of the NDEx network data storage. networks.json is the name of configuration file. public.ndexbio.org is the host name of the NDEx server.

Step 3 Start the Interactome Search service

You can use this command to start the service:

nohup java -Xmx1g -Dndex.host="http://dev.ndexbio.org/v2" -Dndex.interactomehost=dev.ndexbio.org -Dndex.interactomedb=/opt/ndex/services/interactome -Dndex.queryport=8287 
-jar interactomeSearch-<VERSION>.jar & 1>out

The service supports the following command line parameters:

• ndex.host Host name of the NDEx server that this service search on. Default value is public.ndexbio.org.
• ndex.interactomehost Host name of this interactome service. Default value is loalhost.
• ndex.interactomedb Path of the interactome directory. Default value is /opt/ndex/services/interactome.
• ndex.queryport Port number of this service. Default value is 8285.
• ndex.fileRepoPrefix Path of the NDEx network file storage. Default value is /opt/ndex/data/.

Stop the NDEx Interactome Search REST Service

sudo -u ndex /bin/bash # become ndex user
ps -elf | grep interactome
kill <PID of java process for interactome output from previous step>

Rebuild the index

If you edit the configuration file or any of the networks you used in the search is modified in NDEx server, You need to rebuild the index of this service. To rebuild the index.

1. Stop the interactome service
2. Delete the genedb directory in the interactome directory
3. Run the create index command.
4. Start the interactome service.