documentation on how to create and access bio4j db is unclear

[Daniel McClanahan]

Hello,

I'm interested in using Bio4j in a project I'm doing with a few other students at my university over the summer for iGEM (http://2014.igem.org/Software). We were planning to write our own library to crawl and parse protein-protein interaction data from multiple sources, but we were pleased to find bio4j already integrated that functionality and data into a single working database. However, I've been having a devil of a time attempting to figure out which projects in the bio4j github are even relevant to what I'm trying to do.

In short, I want to be able to query the bio4j data to perform some graph algorithms on it. I've looked at the bio4j, neo4jdb, and titandb pages on github, but my progress has been halted by a multitude of issues. The neo4jdb and bio4j dependencies compile in an sbt project, but the instructions to add resolvers and dependencies in the readme for the titandb project end up being unable to find the dependency; not sure why. As another user mentioned in a previous thread, just building the bio4j database doesn't actually work; when following the official instructions at https://github.com/bio4j/bio4j/blob/master/docs/importing-bio4j.md, the process throws a ClassNotFoundException when trying to import InitBio4jDB. The same result happens regardless of which version of DownloadAndPrepareBio4jSources.sh and/or executionsBio4j.xml I use. I perused the other results in this group and tried the solutions shown, with no success.

I've just been having a very rough time even attempting to start using bio4j in my project. If I want the database locally (which I do; I'll be performing quite a few queries on it), do the neo4jdb and titandb packages include that directly? Or do I need to perform the "Importing bio4j" process given in the bio4j project doc? What do I even need to compile?

Mainly, if I want to perform queries on a local bio4j database (I'm planning on using the neo4j backend out of familiarity) in a java program (or a program in any other language that supports cypher/gremlin), what do I need to install to get that functionality working? I am quite frankly lost.

Thanks for the help.

[Pablo Pareja Tobes]

Hi Daniel,

First of all great to hear about your interest in using Bio4j for one of your projects.

Unfortunately, as you are mentioning, the documentation for the current version is a bit confusing and scarce but we're working in a new Bio4j version including major changes and improvements at all levels. 

This work (including good documentation) should be finished in a month tops. Thus I would suggest you to wait for this new version instead of trying to make sense of the one available right now.

Cheers,

Pablo

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[Daniel McClanahan]

Brilliant, I'll keep a watchful eye out for that release. Thanks for the update!