Trying to Use Bio4j for project...How do I start?

[Ayush Gupta]

Hi everyone,

For a class project I'm trying to make a graphical database using orthology and PPI interactions between proteins from several protein families and I was hoping to use Bio4j. I am having a little trouble starting.

Would the best way to be import Bio4j using an AWS? If so, I'm a little confused on how to do this. I followed the instructions (i think) but several of the steps didn't work. For example, when I tried download and install the java jdk it threw me some errors. Also not sure how to get files and edit them. I just did curl -v "url".

Any help would be greatly appreciated!

Thank you!

[Pablo Pareja Tobes]

Hi Ayush,

Great to hear that you're interested in using Bio4j.

If you have the chance to use AWS I would strongly recommend you to simply instantiate a new volume from the official Bio4j 0.8 Snapshot. You can find some information about it here:

https://github.com/bio4j/Bio4j/wiki/Bio4j-0.8

That way you won't have to worry about importing the data yourself ;)

HTH 

Cheers,

Pablo

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[Ayush Gupta]

Thanks.

I got that to work. I am slightly new to all this so sorry if these questions are obvious. So I have the entire database on my own AWS now. Can I remove certain parts of what is provided (because I don't need all these relationships) and then add information from other databases? For example, I only want to keep the information from Uniprot, Gene-ontology, UniRef, and the Protein Interactions. And then I wish to supplement this with information from other databases just as KEGG and PHOG. And how would I go about doing this?

Thanks!

Ayush

[Ayush Gupta]

As far as I understand I can use GNU to interact with the bio4j database? So will I have to download a version into my AWS instance? And then from there I can write code to interact with the database?

Thanks for your help.

[Pablo Pareja Tobes]

Hi Ayush,

Of course you can modify/delete/add new nodes to the database, in the end what you have is just a graph :)

In order to do this you could use the Java API, Gremlin, Cypher... (I'd personally go for the Java API for this sort of operations).

What do you mean by "using GNU to interact with Bio4j"? 

Cheers,

Pablo

[Ayush Gupta]

On your slideshow presentation and on the sample code, it says released through GNU or something? But I guess that's not important.

So if I use eclipse IDE for AWS i just use the com.era7.bioinfo.bio4j... packages and I can interact with the database that I downloaded as I please? And so does this package just get downloaded with the database when I use the snapshot to create a volume on my AWS instance?

Thanks!
Ayush

[Pablo Pareja Tobes]

Hi Ayush,

I guess what you meant is that Bio4j is released under AGPLv3? (this is about code/project licensing).

Yeah, you can simply interact with the DB through the Bio4j Java API using the corresponding classes and methods. 

I think that the jar file including the libraries is included in the snapshot (please let me know if it is not).

Cheers,

Pablo

[Pablo Pareja Tobes]

Hi Ayush,

You're right, in order to import Uniprot in the current version of Bio4j you need to have both EnzymeDB and GO previously imported. This is fixed in the next release. However it's not a big deal since they both are quite "small" resources and shouldn't affect at all the performance of the DB, taking into account that you're importing a decent/large size resource such as Uniprot.

Cheers,

Pablo

On Sat, Apr 27, 2013 at 7:47 AM, Ayush Gupta <theayu...@gmail.com> wrote:

On the module schema is shows that Uniprot is dependent on the EnzymeDB and GO? However, I am interested only in Uniprot and Protein Interactions. So is it allowable to only import those two databses? Or is GO and EnxymeDB required?

Thanks,
Ayush

[Piyush Uthra]

Hi, 

I too am implementing a project on importing database from uniProt and building graphical nodes for finding protein-protein interactions. However, I do not have access to AWS. It would be of great help if someone could assist me in installing Bio4j and its associated modules.

Thank you.

[Pablo Pareja Tobes]

Hi Piyush,

Sorry for the delay but your message got somehow lost in my inbox and I just saw it...

Anyways, as I already said in previous messages, I would recommend you to either use the version 0.9 available in AWS or wait for the new version we're working hard on (it should be available pretty soon)

Cheers,

Pablo

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