[Biojava-l] Load NCBI Taxonomy data using BioJava

Alejandro Rodríguez González alejandro at alejandrorg.com
Tue Mar 17 11:01:31 UTC 2015

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.


Dr. Alejandro Rodríguez González - PhD

Bioinformatics at Centre for Plant Biotechnology and Genomics UPM-INIA
Polytechnic University of Madrid
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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