[Biojava-l] Load NCBI Taxonomy data using BioJava

[Alejandro Rodríguez González]

Hi Michael!

Thank you very much! I've done it. Sadly I saw that the load of names.dmp
and nodes.dmp takes lots of time (well, normally, there are big files) and
in fact with "default parameters" my program ends with an outofmemory error
(I was just trying to load the data and insert all the NCBITaxon objects on
a LinkedList). I was taking a look to the possibility of load the content
of NCBI taxonomy in a database through BioSQL.

Do you think that this could be a best option to manage NCBI Taxonomy data?

Cheers

On 17 March 2015 at 16:28, Michael Heuer <heuermh at gmail.com> wrote:

> Hello Dr. González,
>
> The link below related to the BioJavaX libraries is in fact for the 1.x
> series of BioJava releases (also known as biojava-legacy).
>
> The 1.x download page is here
> http://biojava.org/wiki/BioJava:Download_1.9.1
>
> I just cut a version 1.9.2 last Friday and haven't updated the wiki yet,
> so if you're using Maven, try e.g.
>
>     <dependency>
>       <groupId>org.biojava</groupId>
>       <artifactId>core</artifactId>
>       <version>1.9.2</version>
>     </dependency>
>
> The other jars are listed here, look for version 1.9.2
>
> http://search.maven.org/#search|ga|1|g%3A%22org.biojava%22
> <http://search.maven.org/#search%7Cga%7C1%7Cg%3A%22org.biojava%22>
>
>    michael
>
>
>
> On Tue, Mar 17, 2015 at 6:01 AM, Alejandro Rodríguez González <
> alejandro at alejandrorg.com> wrote:
>
>> Hi all,
>>
>> First of all, apologies if this question has been already answered or
>> seems silly. I'm new using BioJava and I've been trying to do this for a
>> couple of days but I don't find any answer/solution.
>>
>> I just want to load NCBI Taxonomy content (names.dmp and nodes.dmp, as I
>> saw in the documentation (
>> http://biojava.org/wiki/BioJava:BioJavaXDocs#NCBI_Taxonomy_loader.))
>> using BioJava in order to query the taxonomy data.
>>
>> In the wiki I found an example about how to "start" the loading process (
>> http://biojava.org/wiki/BioJava:BioJavaXDocs#NCBI_Taxonomy_data) but I
>> realized that these classes doesn't exists in current Jars. I download all
>> the jars and import all of them (because I didn't know if I only need core
>> or any extra one) but the class is missing. I also see that Javadoc of 4.0
>> version (http://www.biojava.org/docs/api4.0.0/) doesn't have the classes
>> mentioned in the example neither.
>>
>> Searching I found that these classes seem to be classes of an older
>> BioJava version (1.5, 1.7, ..).
>>
>> I don't know if I'm doing something wrong or just is that this part of
>> the wiki has not been updated or..? any clue?
>>
>> If any of you, by the way, have some example of code working with ncbi
>> taxonomy that can provide me it would be very helpful.
>>
>> Cheers
>>
>> --
>> Dr. Alejandro Rodríguez González - PhD
>>
>> Bioinformatics at Centre for Plant Biotechnology and Genomics UPM-INIA
>> Polytechnic University of Madrid
>> http://www.alejandrorg.com
>> Phone: +34 914524900 . Ext: 25550
>>
>>
>> *Once the game is over, the king and the pawn go back in the same box. -
>> Italian proverb*
>>
>> _______________________________________________
>> Biojava-l mailing list  -  Biojava-l at mailman.open-bio.org
>> http://mailman.open-bio.org/mailman/listinfo/biojava-l
>>
>
>


-- 
Dr. Alejandro Rodríguez González - PhD

Bioinformatics at Centre for Plant Biotechnology and Genomics UPM-INIA
Technical University of Madrid
http://www.alejandrorg.com
Phone: +34 914524900 . Ext: 25550


*Once the game is over, the king and the pawn go back in the same box. -
Italian proverb*
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