Using Bio4j + Neo4j Graph-algo component for finding protein-protein interaction paths
From the post:
Today I managed to find some time to check out the Graph-algo component from Neo4j and after playing with it plus Bio4j a bit, I have to say it seems pretty cool.
For those who don’t know what I’m talking about, here you have the description you can find in Neo4j wiki:
This is a component that offers implementations of common graph algorithms on top of Neo4j. It is mostly focused around finding paths, like finding the shortest path between two nodes, but it also contains a few different centrality measures, like betweenness centrality for nodes.
The algorithm for finding the shortest path between two nodes caught my attention and I started to wonder how could I give it a try applying it to the data included in Bio4j.
Suggestions of other data sets where shortest path would yield interesting results?
BTW, isn’t the shortest path an artifact of the basis for nearness between nodes? Thinking that shortest path when expressed between gene fragments as relatedness would be different than physical distance. (see: Nearness key in microbe DNA swaps: Proximity trumps relatedness in influencing how often bacteria pick up each other’s genes.)