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Question about map2slim

Chris Mungall cjm at fruitfly.org
Fri Jan 21 12:32:54 PST 2005


Hi Andy,

Can you send me the exact command line you are using, and the dates you
downloaded the files? I can't replicate the duplicated counts.

Sorry about the bogus error messages - they'll be removed in the next
release

On Fri, 21 Jan 2005, Andrew Nunberg wrote:

> 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
>


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