Protein and accession

[Darèios89]

If i have to search proteins by their synonyms, i think i have to use a code line such as:

List <ProteinNode> proteins = nodeRetriever.getProteinsByFullName(protein);

"protein" is a string with its name. I downloaded the folder uniref50.xml and i put as arg[0] it on Eclipse, but i have exceptions and i don't know why. They are parsing errors but what i have to do if the line code is right? Why there are these exceptions? Maybe it depends on the fact i don't use accessions? I' m desperate...

graphservice hashcode: -1836727

java.lang.RuntimeException: org.apache.lucene.queryParser.ParseException: Cannot parse 'Glycine dehydrogenase [decarboxylating], mitochondrial': Encountered " "]" "] "" at line 1, column 38.

Was expecting one of:

    "TO" ...

    <RANGEIN_QUOTED> ...

    <RANGEIN_GOOP> ...

    

at org.neo4j.index.impl.lucene.IndexType.query(IndexType.java:290)

at org.neo4j.index.impl.lucene.LuceneIndex.query(LuceneIndex.java:226)

at com.era7.bioinfo.bio4j.model.util.NodeRetriever.getProteinsByFullName(NodeRetriever.java:156)

at src.main.java.com.era7.bioinfo.bio4j.drug.Prova.main(Prova.java:136)

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[Darèios89]

I forgot to say i' m on Windows 8.

[Pablo Pareja Tobes]

Hi Dareios,

You should first have a deeper look at the documentation and the project in general because it looks like you're trying to use the DB without even previously importing it...! :)

Please have a look here:

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

in order to see a step-by-step guide on how to import Bio4j into your own machine.

Cheers,

Pablo

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[Darèios89]

I Pablo! I have read the instructions, but i don't understand what the last instruction does, also because i' m on windows and it refers to linux. I have downloaded 
uniprot_sprot.xml and put it as folder of the DB with the code:

String folder="C:\\Users\\Dario\\workspace\\Dbio4j\\src\\src\\main\\java\\com\\era7\\bioinfo\\bio4j\\drug\\uniprot_sprot.xml";

manager = new Bio4jManager(folder);

NodeRetriever nodeRetriever = new NodeRetriever(manager);

Now i think it' s right because i see other files into the uniprot folder....such as...index....neostore....

[Pablo Pareja Tobes]

Hi Dareios,

The importing process for the whole DB takes at least ~ 20 hours in a personal computer. 

Besides, the DB folder should have a size of ~ 100GB if you imported all modules.

Cheers,

Pablo

[Darèios89]

Yes Pablo. ..but i need to do the last passage of importing bio4j? The 8th one. Because i downloaded part of the DB...and i want to know if putting as manager parameter the DB folder let me to search on the DB.

[Pablo Pareja Tobes]

Hi Dareios,

You have to follow all the steps specified here:

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

If you didn't execute step 9 you didn't import anything at all into the DB.

Cheers,

Pablo

On Wed, Apr 24, 2013 at 12:59 PM, Darèios89 <dariog...@gmail.com> wrote:

Yes Pablo. ..but i need to do the last passage of importing bio4j? The 8th one. Because i downloaded part of the DB...and i want to know if putting as manager parameter the DB folder let me to search on the DB.

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[Darèios89]

Thanks...i read at step 9:

"Different log files will be created at jar folder level regarding the progress of the data importation"

Where is exactly this jar folder?

[Pablo Pareja Tobes]

Hi Dareios,

That refers to the folder where you're running the jar file.

Cheers,

Pablo

[Darèios89]

Good, thanks Pablo, i downloaded Bio4jManager and Bio4jTools and i can reach them from the file system, but when i run the instruction:

sudo jdk1.6.0_23/bin/java -d64 -Xmx30G -jar ExecuteBio4jTool.jar executionsBio4j.xml &

I don't indicate a folder, so does it work automatically?

[Pablo Pareja Tobes]

Hi Dareios,

Please have a look at the step: 8b. Tuning executions.xml file

Cheers,

Pablo

[Darèios89]

Hi Pablo, so if i want to inlcude only uniref i think the DownloadAndPrepareBio4jSources should be like this:

curl 'ftp://ftp.uniprot.org/pub/databases/uniprot/uniref/uniref100/uniref100.xml.gz' -o uniref100.xml.gz

curl 'ftp://ftp.uniprot.org/pub/databases/uniprot/uniref/uniref90/uniref90.xml.gz' -o uniref90.xml.gz

curl 'ftp://ftp.uniprot.org/pub/databases/uniprot/uniref/uniref50/uniref50.xml.gz' -o uniref50.xml.gz

gzip -d *.gz

And the execution:

<scheduled_executions>

<execution>

<class_full_name>com.era7.bioinfo.bio4j.programs.InitBio4jDB</class_full_name>

<arguments>

<argument>bio4jdb</argument>

<argument>batchInserter.properties</argument>

</arguments>

</execution>

<execution>

<class_full_name>com.era7.bioinfo.bio4j.programs.ImportUniref</class_full_name>

<arguments>

<argument>uniref100.xml</argument>

<argument>uniref90.xml</argument>

<argument>uniref50.xml</argument>

<argument>bio4jdb</argument>

<argument>batchInserter.properties</argument>

</arguments>

</execution>

</scheduled_executions>

Maybe it is a problem i have a pc with only 1G RAM.

 

[Pablo Pareja Tobes]

Hi Dareios,

Please have a look at the schema shown in step 8b :https://github.com/bio4j/Bio4j/wiki/Importing-bio4j , you need to have Uniprot already imported in your DB prior to import Uniref module.

Yeah, having only 1G RAM could likely be an issue.

Cheers,

Pablo

[Zaynab Mousavian]

Hi,

I have read this conversation, and i have found that you use bio4j DB in Windows.

Is it possible? How can i import this database on Windows OS. In the importing section of Wiki site, the instructions of importing bio4j on a machine with Linux OS only are explained.

Thanks

[Pablo Pareja Tobes]

Hi Zaynab,

The different steps from the importing process in both Windows and Linux are virtually the same. 

Since Java is a multi-platform language and the DB system is embedded in the jar file your only requirement in order to import the last version of Bio4j is having installed Java 7.

Apart from that, the only thing I can think about that would be different depending on your OS choice is that you'll have to use equivalent programs in windows to download some of the files through FTP or decompress/extract the .gz files.

Cheers,

Pablo

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