<div dir="ltr"><div><div><div>Hello Dr. González,<br><br></div>The link below related to the BioJavaX libraries is in fact for the 1.x series of BioJava releases (also known as biojava-legacy).<br><br></div>The 1.x download page is here<br><a href="http://biojava.org/wiki/BioJava:Download_1.9.1">http://biojava.org/wiki/BioJava:Download_1.9.1</a><br><br>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.<br><pre> <dependency>
<groupId>org.biojava</groupId>
<artifactId>core</artifactId>
<version>1.9.2</version>
</dependency></pre>The other jars are listed here, look for version 1.9.2<br><br><a href="http://search.maven.org/#search|ga|1|g%3A%22org.biojava%22">http://search.maven.org/#search|ga|1|g%3A%22org.biojava%22</a><br><br></div><div> michael<br></div><div><br></div><div><div><br></div></div></div><div class="gmail_extra"><br><div class="gmail_quote">On Tue, Mar 17, 2015 at 6:01 AM, Alejandro Rodríguez González <span dir="ltr"><<a href="mailto:alejandro@alejandrorg.com" target="_blank">alejandro@alejandrorg.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Hi all,<div><br></div><div>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.</div><div><br></div><div>I just want to load NCBI Taxonomy content (names.dmp and nodes.dmp, as I saw in the documentation (<a href="http://biojava.org/wiki/BioJava:BioJavaXDocs#NCBI_Taxonomy_loader." target="_blank">http://biojava.org/wiki/BioJava:BioJavaXDocs#NCBI_Taxonomy_loader.</a>)) using BioJava in order to query the taxonomy data.</div><div><br></div><div>In the wiki I found an example about how to "start" the loading process (<a href="http://biojava.org/wiki/BioJava:BioJavaXDocs#NCBI_Taxonomy_data" target="_blank">http://biojava.org/wiki/BioJava:BioJavaXDocs#NCBI_Taxonomy_data</a>) 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 (<a href="http://www.biojava.org/docs/api4.0.0/" target="_blank">http://www.biojava.org/docs/api4.0.0/</a>) doesn't have the classes mentioned in the example neither.</div><div><br></div><div>Searching I found that these classes seem to be classes of an older BioJava version (1.5, 1.7, ..).</div><div><br></div><div>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?</div><div><br></div><div>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.</div><div><br></div><div>Cheers<span class="HOEnZb"><font color="#888888"><br clear="all"><div><br></div>-- <br><div><span style="font-family:'Times New Roman';font-size:medium">Dr. Alejandro Rodríguez González - PhD<br style="padding:0px;margin:0px"><br style="padding:0px;margin:0px"><div>Bioinformatics at Centre for Plant Biotechnology and Genomics UPM-INIA</div><div>Polytechnic University of Madrid</div><a href="http://www.alejandrorg.com" target="_blank">http://www.alejandrorg.com</a><br style="padding:0px;margin:0px">Phone: +34 </span><font face="Times New Roman" size="3">914524900 . Ext: 25550</font><div><span style="font-family:'Times New Roman';font-size:medium"><br></span></div><div><span style="font-family:'Times New Roman';font-size:medium"><br></span></div><div><span style="font-family:'Times New Roman';font-size:medium"><i>Once the game is over, the king and the pawn go back in the same box. - Italian proverb</i></span></div></div>
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