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cogat-neo4j

Testing the Cognitive Atlas as a neo4j graph

1. Download neo4j

the community edition of neo4j. On linux this means extracting the binary to somewhere on your computer:

  cd $HOME/Downloads
  mv neo4j-community-2.2.5-unix.tar.gz $HOME/Packages/
  tar -xzvf neo4j-community-2.2.5-unix.tar.gz 
  rm neo4j-community-2.2.5-unix.tar.gz

2. Add to path

To add to your path:

  vim ~/.bashrc
  export PATH=$PATH:/home/vanessa/Packages/neo4j-community-2.2.5/bin
  source ~/.bashrc
  which neo4j
  /home/vanessa/Packages/neo4j-community-2.2.5/bin/neo4j

Then start the server

  neo4j start

Open browser to http://localhost:7474/ to see the server running.

3. Download

Set a new password

You will see a login screen, and instructions to log in with the old password, "neo4j." Log in and you will be prompted to set a new password. Don't forget it, you will need it to test the script.

4. Download

Make sure you have the cognitive atlas python API wrapper installed. Also install py2neo, which is the module for working with neo4j from Python.

  pip install py2neo --user

5. Authenticate

Next, go through the lines of the script mk_cogat_neo4j.py. When it gets to the line:

  authenticate("localhost:7474", "neo4j", "neo4j")

this is where you will need to change your password to the one you just set. The authentication doesn't happen at this step, it will happen when you try to make the graph:

  graph = Graph()

so if there are authentication errors you will see them at this time point.

You should be able to run through the code, and see that the interface updates. The Cognitive Atlas API python wrapper spits out a lot of text, so be prepared for that. If the interface in the web browser doesn't update, click the circles in the left bar to see your graph nodes (or click monitor) and in the bottom right of the box that shows your graph (db/data) statistics, click the slider that says "auto refresh." Note that if you need to wipe the entire thing any time, just rm -rf db/data.

Exploration needed

The work has only been done to set up the skeleton for a graph! We want to know if Cognitive Atlas would be good to have in neo4j, so these are the questions we want to explore with this test:

  • what kind of queries would I run, and what do they look like in neo4j?
  • how easy/hard is it to add/delete/modify the graph?
  • how easy is it to visualize the graph, or integrate into a web project?
  • what about an API?