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bio4j/bio4j

Bio4j abstract model and general entry point to the project

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Oct 12 15:44

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Dec 16 2016 10:50

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Eduardo Pareja Tobes

@eparejatobes

it would be really easy to do

We only need a working angulillos implementation for Neo4j

I played a bit with it one year ago

https://github.com/bio4j/angulillos-neo4j

the only issue I found was indexes

the Neo4j API was in a transitioning state

maybe things improved a bit there, didn't check

but nothing insurmountable

cosimosimeoneTR

@cosimosimeoneTR

@eparejatobes Thanks a ton!
Yep, i have same needs (HUGE datasets) and i was having trouble with relativeli small (20m nodes) dataset with Neo4j...

Sandra Castillo

@SandraCastilloPriego

I have several projects.. One of them is related with protein similarities. We are trying to compute a big protein similarity matrix using all the proteins found in uniprot and other db. With it we are planning to apply some clustering methods and do some data mining

Sandra Castillo

@SandraCastilloPriego

Also, we are creating metabolic models of different organisms

Eduardo Pareja Tobes

@eparejatobes

@SandraCastilloPriego sorry got to leave yesterday

I see

yep, Bio4j sounds like a good fit for that

I think that you'd only need to import data locally

and use the Bio4j API

which is backend-independent

if you prefer to discuss it in private send me an email or private chat here

Fadel

@FadelBerakdar

Is there any python API for Bio4j ? if not how much java should I know before i start a simple bio4j project ?

Fadel

@FadelBerakdar

btw Im undergraduate student and I chose a topic related to Bio4j to do my final year project :D
sounds crazy but yeah I will do it :D

Alexey Alekhin

@laughedelic

@FadelBerakdar hi!
There is no Python API for Bio4j. But I believe, that you don't really need any Java knowledge to start with Bio4j :wink:
The current version uses TitanDB v0.5.4 as a backend (see bio4j-titan repo). So you can interact with the database in a number of ways:

through the Bio4j Java API :sparkles:
through the raw TitanDB Java API
through the Tinkerpop/Gremlin API, for which, I think, there are various implementations including Python (probably this?).

Anyway, it may be good for starting with it, but if you are really going to do something serious with Bio4j, it's worth using the Bio4j Java API (we are also working on a Scala version), because it let's you to take advantage of the quite complex schema of the database :+1:

Fadel

@FadelBerakdar

thanks @laughedelic,
I still have some simple questions if u don't mind :)

Fadel

@FadelBerakdar

like
I couldn't find RefSeq module in bio4j-lite nor bio4j-full !
500 GB is the size of bio4j-lite.tar or Bio4j-lite ? sorry if u found my questions quite naive, I'm just trying to figure out how much exactly the AWS will cost me :'(

Alexey Alekhin

@laughedelic

@FadelBerakdar, I think about AWS is better to ask @eparejatobes

Eduardo Pareja Tobes

@eparejatobes

sorry didn't get notifications :(

@FadelBerakdar

About AWS

the required size would be less than 1TB for full

speaking from memory though

so could be wrong

about costs in general:

if you work in eu-west-1, all data transfer is free
you can always find instance types with enough (ephemeral) instance store space so that Bio4j will fit there

in that scenario, your costs will only be EC2-based.

Fadel

@FadelBerakdar

sounds great ... thanks @eparejatobes

Fadel

@FadelBerakdar

hey there :)
I just have one simple question and I couldn't find an answer ... how the data is being updated?

Fadel

@FadelBerakdar

This message was deleted

I mean how I can update the data after transferring it to my AWS instance ?

Alexey Alekhin

@laughedelic

@FadelBerakdar hi. What do you mean by "updating data"? You mean how to import Bio4j with updated raw data?

Fadel

@FadelBerakdar

sorry for this ambiguous question, lets say I import the raw dat to my AWS instance, and after one year I want to update my database, since all those original biological databases are being updated from time to time. Is ur bio4j raw data being updated frequently?

Alexey Alekhin

@laughedelic

@FadelBerakdar sorry, I forgot to reply :sweat_smile:

If you want to update the data, you need to reimport_ everything _from the scratch. There is no way of updating an existing database (data migration problems, changing formats of the source data, etc.)

Alexey Alekhin

@laughedelic

So you can follow import instructions in bio4j-titan, if you want to do it yourself.

Or you can wait a bit, because right now we are working on a big update: migrating to TitanDB-1.0 and simplifying the Bio4 Java API. Once we finish with the code refactoring, we'll import the latest source databases and make releases with ready-to-use Bio4j-TitanDB :wink:

Fadel

@FadelBerakdar

thats great news :fire: thanks a lot guys :)

Alexey Alekhin

@laughedelic

We'll keep you updated here :wink: :ok_hand:

jonathan MERCIER

@bioinfornatics

Dear, I try to run code example https://github.com/bio4j/bio4j-examples/blob/master/src/main/java/com/bio4j/examples/enzyme/GetProteinEnzymaticActivity.java#L73 but the line 73 do not want to compile. As Object Unique<Protein...> do not have a method named getVertex. I think the latest api have some change. No ?

jonathan MERCIER

@bioinfornatics

can not resolve getVertex(java.lang.String)

jonathan MERCIER

@bioinfornatics

And I if comment lines from 73 to 88. Run the example with properties https://github.com/bio4j/bio4j-examples/blob/master/getProteinEnzymaticActivity.properties an error is raised: Exception in thread "main" java.lang.IncompatibleClassChangeError: Implementing class at line 62

Marina Manrique

@marina-manrique

This message was deleted

Yasset Perez-Riverol

@ypriverol

@hi, is this project still active?