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Question about map2slim

Andrew Nunberg anunberg at oriongenomics.com
Fri Jan 21 09:54:26 PST 2005


I have tried to run map2lim to map a collection of proteins  of interest to
the generic go slim to make a pie chart.

When running map2lim I get errors from parsing  the ontology file, here is
an example
<error>
    <message>missing namespace for ID: GO:0008291</message>
    <file>gene_ontology.obo</file>
    <parse_class>GO::Parsers::obo_text_parser</parse_class>
  </error>

I used the ­c  option to get a count, but I have noticed that some of the
slim terms are repeated
Eg.
GO:0016049 cell growth (cell growth)    4       4
biological_process
GO:0009790 embryonic development (embryonic development)        3       3
biologic
al_process
GO:0040007 growth (growth)      1       5               biological_process
GO:0016049 cell growth (cell growth)    4       4
biological_process
GO:0009653 morphogenesis (morphogenesis)        21      24
biological_process
GO:0016049 cell growth (cell growth)    4       4
biological_process

Am I doing something wrong?

Andy
-- 
Andrew Nunberg
Bioinformagician
Orion Genomics
(314)-615-6989
www.oriongenomics.com


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