<div dir="ltr">Hi Michael!<div><br></div><div>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.</div><div><br></div><div>Do you think that this could be a best option to manage NCBI Taxonomy data?</div><div><br></div><div>Cheers</div></div><div class="gmail_extra"><br><div class="gmail_quote">On 17 March 2015 at 16:28, Michael Heuer <span dir="ltr"><<a href="mailto:heuermh@gmail.com" target="_blank">heuermh@gmail.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"><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" target="_blank">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%7Cga%7C1%7Cg%3A%22org.biojava%22" target="_blank">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"><div><div class="h5">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></div></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div class="h5"><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><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"><a href="tel:914524900" value="+34914524900" target="_blank">914524900</a> . 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>
</font></span></div></div>
<br></div></div>_______________________________________________<br>
Biojava-l mailing list - <a href="mailto:Biojava-l@mailman.open-bio.org" target="_blank">Biojava-l@mailman.open-bio.org</a><br>
<a href="http://mailman.open-bio.org/mailman/listinfo/biojava-l" target="_blank">http://mailman.open-bio.org/mailman/listinfo/biojava-l</a><br></blockquote></div><br></div>
</blockquote></div><br><br clear="all"><div><br></div>-- <br><div class="gmail_signature"><div dir="ltr"><div><span style="font-family:'Times New Roman';font-size:medium">Dr. Alejandro Rodríguez González - PhD<br style="padding-top:0px;padding-right:0px;padding-bottom:0px;padding-left:0px;margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0px"><br style="padding-top:0px;padding-right:0px;padding-bottom:0px;padding-left:0px;margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0px"><div>Bioinformatics at Centre for Plant Biotechnology and Genomics UPM-INIA</div><div>Technical University of Madrid</div><a href="http://www.alejandrorg.com" target="_blank">http://www.alejandrorg.com</a><br style="padding-top:0px;padding-right:0px;padding-bottom:0px;padding-left:0px;margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left: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></div></div>
</div>