[Bioperl-l] bioperl-db

David Burt david at burt7259.freeserve.co.uk
Sat Apr 12 17:01:57 UTC 2008

Hi Hilmar,

Hope you can help – I am using bioperl-db to create a biosql database

I have used scripts load_seqdatabase.pl and load_ontology.pl to  
install human swissprot entries, gene ontology, sequence ontology and  
now want to load interpro

Here’s the command line I have tried

perl load_ontology.pl --host --dbname bioseqdb --dbuser  
root --dbpass chicken --driver mysql \
--namespace "InterPro" --format InterPro interpro.xml

But I get this message

Can't call method "identifier" on an undefined value at  /cygdrive/c/ 
SimpleOntologyEngine.pm line 395

Any ideas?


PS: here’s the top of the interpro.xml file

<?xml version="1.0" encoding="ISO-8859-1"?>
<!DOCTYPE interprodb SYSTEM "interpro.dtd">

       <dbinfo dbname="PANTHER" version="6.1" entry_count="30128"  
file_date="04-OCT-2006 00:00:00" />
       <dbinfo dbname="PFAM" version="21.0" entry_count="8957"  
file_date="22-NOV-2006 00:00:00" />
       <dbinfo dbname="PIRSF" version="2.70" entry_count="2877"  
file_date="12-JUN-2007 00:00:00" />
       <dbinfo dbname="PRINTS" version="38.0" entry_count="1900"  
file_date="22-SEP-2005 00:00:00" />
       <dbinfo dbname="PRODOM" version="2005.1" entry_count="1522"  
file_date="23-APR-2004 00:00:00" />
       <dbinfo dbname="PROSITE" version="20.0" entry_count="2006"  
file_date="14-NOV-2006 00:00:00" />
       <dbinfo dbname="SMART" version="5.1" entry_count="724"  
file_date="27-JUL-2007 00:00:00" />
       <dbinfo dbname="TIGRFAMs" version="7.0" entry_count="3423"  
file_date="28-SEP-2007 00:00:00" />
       <dbinfo dbname="GENE3D" version="3.0.0" entry_count="2147"  
file_date="11-SEP-2006 00:00:00" />
       <dbinfo dbname="SSF" version="1.69" entry_count="1538"  
file_date="30-NOV-2006 00:00:00" />
       <dbinfo dbname="SWISSPROT" version="55.1" entry_count="359942"  
file_date="18-MAR-2008 00:00:00" />
       <dbinfo dbname="TREMBL" version="38.1" entry_count="5443281"  
file_date="18-MAR-2008 00:00:00" />
       <dbinfo dbname="INTERPRO" version="17.0" entry_count="16175"  
file_date="19-MAR-2008 00:00:00" />
       <dbinfo dbname="GO" version="N/A" entry_count="23937"  
file_date="27-MAR-2007 00:00:00" />
       <dbinfo dbname="MEROPS" version="7.8" entry_count="2831"  
file_date="12-JUL-2007 16:56:17" />
   <interpro id="IPR000001" type="Domain" short_name="Kringle"  


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