About

Pathway Commons Simple Network Visualizer, PCViz in short.

Use

Clone the repository and change (cd) in there.

Copy and edit the configuration file:

cp -f src/main/resources/application.properties.example src/main/resources/application.properties

The property hgnc.location should point to a valid HGNC output that contains the official gene symbols and their synonyms. This file can be downloaded as follows:

wget -O /tmp/hgnc.txt "https://www.genenames.org/cgi-bin/download/custom?col=gd_app_sym&col=gd_aliases&col=md_prot_id&status=Approved&status_opt=2&where=&order_by=gd_hgnc_id&format=text&limit=&hgnc_dbtag=on&submit=submit"

The property ncbigene.location should point to a valid NCBI (Entrez) Gene output that contains the official gene symbols and IDs. This file can be downloaded as follows:

wget -O /tmp/ncbigene.txt "https://www.genenames.org/cgi-bin/download/custom?col=gd_app_sym&col=gd_pub_eg_id&status=Approved&status_opt=2&where=&order_by=gd_app_sym_sort&format=text&limit=&hgnc_dbtag=on&submit=submit"

Make sure all other properties reflect the options you wanted to set.

Now, build the java application with maven using the following command:

mvn clean package

The following command starts the application:

java -Xmx16g -jar target/pcviz*.jar

or

mvn spring-boot:run

and then point your browser to http://localhost:8080/.

Pre-populate cache (optional)

To serve networks better, PCViz can utilize cached network data. The data folder for the cache files is set within the properties file using the

TODO: it won't cache co-citations due to iHope service is discontinued (we're still looking for other options)

To prepare those caches, you need to

1. Clean up your cache.folder
2. Deploy a dummy PCViz with empty caches
3. Edit uniprot_scraper.js to point to the non-cached version of PCViz (if it is different than the production one)
4. Make sure phantomjs is installed and run uniprot_scraper.sh with these arguments: bash uniprot_scraper.sh /path/to/hgnc.txt /path/to/cache log.txt
5. Move all the JSONs over to your cache.folder/networks/ directory
6. Restart/re-deploy PCViz with this cache folder populated

It is a good idea to clean up other cache folders (such as portal and co-citations) once in a while, but it is not required unless the formatting changes for those files/services. Only the pre-calculated network cache requires pre-processing.