<font size=2 face="sans-serif">Hi Hilmar,</font>
<br>
<br><font size=2 face="sans-serif">Thanks for your reply. Yes, I did try
using --download option, but failed because: 1. load_itis_taxonomy.pl
doesn't support proxy specified; 2. there is no more file like itisMSxxxxxx.TAR.gz
(xxxxxx is date) at site </font><a href=http://www.itis.gov/downloads/><font size=2 face="sans-serif">http://www.itis.gov/downloads/</font></a><font size=2 face="sans-serif">
as specified in load_itis_taxonomy.pl. </font>
<br><img src=cid:_1_06CCE2C006CCDEC000270C3F48257A91>
<br><font size=2 face="sans-serif"> See the screen shot of </font><a href=http://www.itis.gov/downloads:><font size=2 face="sans-serif">http://www.itis.gov/downloads:</font></a>
<br>
<br><img src=cid:_1_06CD0C3006CD0AE000270C3F48257A91>
<br>
<br><font size=2 face="sans-serif">So instead, I manually downloaded
itisMSSql.zip, itisMySQLBulk.zip and itisMySQLTables.tar.gz, uncompress
them in a directory and then ran load_itis_taxonomy.pl with --directory
option. The result as I mentioned in my previous email--I couldn't
find itisMSforTar.sql in any data set tarball.</font>
<br>
<br><font size=2 face="sans-serif">Is it because ITIS has changed its data
set structure (schema) and no more itisMSforTar.sql existed?</font>
<br>
<br><font size=2 face="sans-serif">Thanks,</font>
<br><font size=2 face="sans-serif">MJ Shen</font>
<br>
<br>
<br>
<table width=100%>
<tr valign=top>
<td><font size=1 color=#5f5f5f face="sans-serif">From:</font>
<td><font size=1 face="sans-serif">Hilmar Lapp <hlapp@drycafe.net></font>
<tr valign=top>
<td><font size=1 color=#5f5f5f face="sans-serif">To:</font>
<td><font size=1 face="sans-serif">Mo_Jun_Shen@bd.com</font>
<tr>
<td valign=top><font size=1 color=#5f5f5f face="sans-serif">Cc:</font>
<td><font size=1 face="sans-serif">"biosql-l@lists.open-bio.org"
<biosql-l@lists.open-bio.org></font>
<tr valign=top>
<td><font size=1 color=#5f5f5f face="sans-serif">Date:</font>
<td><font size=1 face="sans-serif">10/08/2012 10:46 AM</font>
<tr valign=top>
<td><font size=1 color=#5f5f5f face="sans-serif">Subject:</font>
<td><font size=1 face="sans-serif">Re: [BioSQL-l] PhyloDB</font></table>
<br>
<hr noshade>
<br>
<br>
<br><font size=3>MJ,</font>
<br>
<br><font size=3>Did you try using the --download option? BTW you can obtain
documentation of this and other options by supplying --help on the command
line.</font>
<br>
<br><font size=3>-hilmar</font>
<br>
<br><font size=3>On Oct 7, 2012, at 10:35 PM, </font><a href=mailto:Mo_Jun_Shen@bd.com><font size=3 color=blue><u>Mo_Jun_Shen@bd.com</u></font></a><font size=3>
wrote:</font>
<br>
<br><font size=2 face="sans-serif">Hi Hilmar,</font><font size=3> <br>
</font><font size=2 face="sans-serif"><br>
Thank you for your reply. I ever tried to run 'load_itis_taxonomy.pl' to
load ITIS taxonomy. But the load_itis_taxonomy.pl could not work
because it needs 'itisMSforTar.sql' to complete the process. When
I run the load_itis_taxonomy.pl, I got error message:</font><font size=3>
<br>
</font><font size=2 color=blue face="sans-serif"><br>
failed to open /itisMSforTar.sql for reading: No such file or directory
</font><font size=3><br>
</font><font size=2 face="sans-serif"><br>
I couldn't find itisMSforTar.sql anywhere. It is neither in BioSQL scripts/sql,
nor in ITIS data set. Can you please advise where I can get itisMSforTar.sql?</font><font size=3>
<br>
</font><font size=2 face="sans-serif"><br>
Thanks,</font><font size=3> </font><font size=2 face="sans-serif"><br>
MJ Shen</font><font size=3> <br>
<br>
</font>
<table width=100%>
<tr valign=top>
<td width=14%><font size=1 color=#5f5f5f face="sans-serif">From:</font><font size=3>
</font>
<td width=85%><font size=1 face="sans-serif">Hilmar Lapp <</font><a href=mailto:hlapp@drycafe.net><font size=1 color=blue face="sans-serif"><u>hlapp@drycafe.net</u></font></a><font size=1 face="sans-serif">></font><font size=3>
</font>
<tr valign=top>
<td><font size=1 color=#5f5f5f face="sans-serif">To:</font><font size=3>
</font>
<td><font size=1 face="sans-serif">"</font><a href=mailto:Mo_Jun_Shen@bd.com><font size=1 color=blue face="sans-serif"><u>Mo_Jun_Shen@bd.com</u></font></a><font size=1 face="sans-serif">"
<</font><a href=mailto:Mo_Jun_Shen@bd.com><font size=1 color=blue face="sans-serif"><u>Mo_Jun_Shen@bd.com</u></font></a><font size=1 face="sans-serif">></font><font size=3>
</font>
<tr>
<td valign=top><font size=1 color=#5f5f5f face="sans-serif">Cc:</font><font size=3>
</font>
<td><font size=1 face="sans-serif">"</font><a href="mailto:biosql-l@lists.open-bio.org"><font size=1 color=blue face="sans-serif"><u>biosql-l@lists.open-bio.org</u></font></a><font size=1 face="sans-serif">"
<</font><a href="mailto:biosql-l@lists.open-bio.org"><font size=1 color=blue face="sans-serif"><u>biosql-l@lists.open-bio.org</u></font></a><font size=1 face="sans-serif">></font><font size=3>
</font>
<tr valign=top>
<td><font size=1 color=#5f5f5f face="sans-serif">Date:</font><font size=3>
</font>
<td><font size=1 face="sans-serif">09/19/2012 02:20 PM</font><font size=3>
</font>
<tr valign=top>
<td><font size=1 color=#5f5f5f face="sans-serif">Subject:</font><font size=3>
</font>
<td><font size=1 face="sans-serif">Re: [BioSQL-l] PhyloDB</font></table>
<br><font size=3><br>
</font>
<hr noshade><font size=3><br>
<br>
<br>
MJ, <br>
<br>
Apologies for the long time your message was held up in moderation. Was
your question resolved meanwhile? There is a script that comes with Biosql
that loads the ITIS taxonomy (which essentially consists of 5 trees, one
for each "kingdom") into the PhyloDB tables. This may serve as
an example for how to get data into those tables. Does this answer your
question?<br>
<br>
-hilmar <br>
<br>
Sent with a tap. <br>
<br>
On Jul 8, 2012, at 9:06 PM, </font><a href=mailto:Mo_Jun_Shen@bd.com><font size=3 color=blue><u>Mo_Jun_Shen@bd.com</u></font></a><font size=3>
wrote:<br>
</font><font size=2 face="sans-serif"><br>
Dear Sir/Madam,</font><font size=3> </font><font size=2 face="sans-serif"><br>
<br>
I am very interested in PhyloDB in BioSQL for querying taxonomy. However,
I couldn't find scripts or document to describe how to setup data for phyloDB
after initiating phyloDB . Could you please provide guidance?<br>
<br>
Thank you.</font><font size=3> </font><font size=2 face="sans-serif"><br>
<br>
Best Regards,</font><font size=3> </font><font size=2 face="sans-serif"><br>
MJ Shen</font><font size=3><br>
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<br><font size=3>-- </font>
<br><font size=3>===========================================================</font>
<br><font size=3>: Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot
net :</font>
<br><font size=3>===========================================================</font>
<br>
<br><font size=3><br>
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