[BioC] KEGG pathway IDs ,issing

[Marc Carlson]

Hi Daniel,

Yes.  We rebuild all of the annotation packages for each new release
(which happens twice a year).  The new KEGG.db has the term you found
and will be available in a matter of days as part of the new release.


  Marc



Daniel Brewer wrote:
> Dear list,
>
> I am fiddling around with KEGG.db and KEGGSOAP and I am finding that
> some of the networkd in KEGG.db are not available through the KEGGSOAP
> API.  FOr example,
>
> hsa05030 : Amyotrophic lateral sclerosis (ALS)
>
> When I search for the name on the KEGG website I get a different number
> e.g. hsa05014.
>
> Is this because the KEGG.db annotation package is old?
>
>   
>> sessionInfo()
>>     
> R version 2.8.1 (2008-12-22)
> i386-apple-darwin8.11.1
>
> locale:
> en_GB.UTF-8/en_GB.UTF-8/C/C/en_GB.UTF-8/en_GB.UTF-8
>
> attached base packages:
> [1] tools     stats     graphics  grDevices utils     datasets  methods
> [8] base
>
> other attached packages:
>  [1] KEGG.db_2.2.5       org.Hs.eg.db_2.2.6  RSQLite_0.7-1
>  [4] DBI_0.2-4           AnnotationDbi_1.4.3 Biobase_2.2.2
>  [7] KEGGSOAP_1.16.0     SSOAP_0.4-6         RCurl_0.94-1
> [10] XML_2.3-0           reshape_0.8.2       plyr_0.1.5
>
> Thanks
>
> Dan
>
>