Hi Ed,

I think that the answer you are looking for is that "they are both". 
KEGGPATHID2EXTID maps "KEGG IDs" to "gene IDs" for a wide range of 
specific organisms.  When KEGG was a new package, the KEGG style 
organism prefixes were left pre-pended on these IDs to emphasize this 
detail.  So the example below shows some of the gene IDs from human 
(hsa).  But if you look at ALL of the IDs, you will find some that map 
to other organisms as well (and these have different prefixes).  Also, 
you may notice that not all of the KEGG pathway IDs will necessarily be 
represented in KEGGPATHID2EXTID.  There is of course substantial 
overlap, but it's worth mentioning that being matched to a gene ID is 
not a prerequisite for being a KEGG ID.


   Marc




On 07/07/2012 08:40 PM, Ed wrote:
> Hi Marc,
>
> KEGGPATHID2EXTID maps KEGG pathway identifiers to Entrez Gene 
> identifiers and the followings are the examples for those identifiers. 
> I guess the over 3000 identifiers are from different organisms instead 
> of they are gene IDs.
>
> > xx <- as.list(KEGGPATHID2EXTID)
> > head(names(xx), 20)
>  [1] "hsa00232" "hsa00983" "hsa01100" "hsa00230" "hsa05340" "hsa04514"
>  [7] "hsa05412" "hsa04010" "hsa04012" "hsa04062" "hsa04150" "hsa04210"
> [13] "hsa04370" "hsa04380" "hsa04510" "hsa04530" "hsa04620" "hsa04630"
> [19] "hsa04660" "hsa04662"
>
>
> On Fri, Jul 6, 2012 at 1:07 AM, Marc Carlson <mcarlson@fhcrc.org 
> <mailto:mcarlson@fhcrc.org>> wrote:
>
>     Hi Ed,
>
>     The confusion is because you have an "apples to oranges"
>     comparison here.  There are 390 unique KEGG IDs in the DB.  That
>     means that there are only 390 KEGG names for those pathways.
>      However, those pathway IDs are matched up to over 3000 different
>     external gene IDs which is why the second mapping is so much
>     larger.  You can learn more about the different mappings by
>     reading their manual pages like this:
>
>     help("KEGGPATHID2NAME")
>
>     help("KEGGPATHID2EXTID")
>
>
>       Marc
>
>
>
>     >
>
>
>     On 07/05/2012 12:48 AM, Ed wrote:
>
>         Hi there,
>
>         I found the number of pathways in KEGGPATHID2NAME is 390 while
>         that
>         in KEGGPATHID2EXTID is 3152. Am I missing something? BTW, the
>         pathway id's
>         used in this package seems inconsistent too.
>
>         Thanks.
>
>         Ed
>
>             ?KEGGPATHID2NAME
>                           xx<- as.list(KEGGPATHID2NAME)
>                           if(length(xx)>  0){
>
>         +                      # get the value for the first key
>         +                      xx[[1]]
>         +                      # Get the values for a few keys
>         +                      if(length(xx)>= 3){
>         +                              xx[1:3]
>         +                      }
>         +              }
>         $`00010`
>         [1] "Glycolysis / Gluconeogenesis"
>
>         $`00020`
>         [1] "Citrate cycle (TCA cycle)"
>
>         $`00030`
>         [1] "Pentose phosphate pathway"
>
>             length(xx)
>
>         [1] 390
>
>
>         ?KEGGPATHID2EXTID
>                       xx<- as.list(KEGGPATHID2EXTID)
>                       if(length(xx)>  0){
>                               # Get the value of the first key
>                               xx[[1]]
>                               # Get the values for multiget for a few keys
>                               if(length(xx)>= 3){
>                                       xx[1:3]
>                               }
>                       }
>
>             length(xx)
>
>         [1] 3152
>
>             sessionInfo()
>
>         R version 2.14.1 (2011-12-22)
>         Platform: x86_64-pc-mingw32/x64 (64-bit)
>
>         locale:
>         [1] LC_COLLATE=Chinese (Simplified)_People's Republic of China.936
>         [2] LC_CTYPE=Chinese (Simplified)_People's Republic of China.936
>         [3] LC_MONETARY=Chinese (Simplified)_People's Republic of
>         China.936
>         [4] LC_NUMERIC=C
>         [5] LC_TIME=Chinese (Simplified)_People's Republic of China.936
>
>         attached base packages:
>         [1] stats     graphics  grDevices utils     datasets  methods
>           base
>
>         other attached packages:
>         [1] KEGG.db_2.6.1         RSQLite_0.11.1        DBI_0.2-5
>         [4] AnnotationDbi_1.16.18 Biobase_2.14.0
>
>         loaded via a namespace (and not attached):
>         [1] IRanges_1.12.5 tools_2.14.1
>
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>
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