[Biojava-l] Load NCBI Taxonomy data using BioJava

[Michael Heuer]

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

   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*
>
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>
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