GRIP

https://bmeg.github.io/grip/

GRIP stands for GRaph Integration Platform. It provides a graph interface on top of a variety of existing database technologies including: MongoDB, PostgreSQL, MySQL, MariaDB, Badger, and LevelDB.

Properties of an GRIP graph:

• Both vertices and edges in a graph can have any number of properties associated with them.
• There are many types of vertices and edges in a graph. Thus two vertices may have myriad types of edges connecting them reflecting myriad types of relationships.
• Edges in the graph are directed, meaning they have a source and destination.

GRIP also provides a query API for the traversing, analyzing and manipulating your graphs. Its syntax is inspired by Apache TinkerPop. Learn more here.

Pathway Commons

To load Pathway commons into a local instance of GRIP, first download the Pathway commons source file.

curl -O https://www.pathwaycommons.org/archives/PC2/v12/PathwayCommons12.All.BIOPAX.owl.gz

Start grip server (using Pebble driver)

grip server --driver=pebble

In another terminal, create the graph

grip create pc12

And load the file, using the RDF loader

grip rdf --gzip pc12 PathwayCommons12.All.BIOPAX.owl.gz -m "http://www.biopax.org/release/biopax-level3.owl#=" -m "http://pathwaycommons.org/pc12/#=pc12:"

Once the graph has been loaded into the database, you can view all of the different vertex and edge types in the graph:

grip list labels pc12

Or run an example query, such as count all of the pathways:

grip query pc12 'V().hasLabel("Pathway").count()'