[BioC] Why are there different number of pathways in pathway2gene and in pathway2name (KEGG.db)?

[Marc Carlson]

Hi Peng,

It's because of the way that the database was built.  The data in 
pathway to gene is limited to those organisms that we produce annotation 
packages for here.

   Marc


On 10/12/2011 02:39 PM, Peng Yu wrote:
> Hi,
>
> There are 292 pathways according to pathway2gene, but there are 390
> pathways according to pathway2name. I'm wondering why these two
> numbers are not the same.
>
>> library(KEGG.db)
>> pathway2gene=dbGetQuery(KEGG_dbconn(), "SELECT * FROM pathway2gene")
>>
>> species=unique(substr(unique(pathway2gene$pathway_id),1,3))
>> species
>   [1] "hsa" "ath" "dme" "mmu" "rno" "sce" "pfa" "dre" "eco" "ecs" "cfa" "bta"
> [13] "cel" "ssc" "gga" "mcc" "xla" "aga" "ptr"
>> tmp=lapply(
> +   species
> +   , function(x) {
> +     unique(pathway2gene$pathway_id[grep(paste('^', x,sep=''),
> pathway2gene$pathway_id)])
> +   }
> +   )
>> sapply(tmp, length)
>   [1] 229 123 127 225 225  99  80 155 105 107 224 225 125 225 152 225 150 126 225
>> tmp1=unique(
> +   unlist(
> +     lapply(
> +       tmp
> +       , function(x) {
> +         substr(x, 4, 8)
> +       }
> +       )
> +     )
> +   )
>> length(tmp1)
> [1] 292
>
>
>> pathway2name=dbGetQuery(KEGG_dbconn(), 'SELECT * FROM pathway2name')
>> length(unique(pathway2name$path_id))
> [1] 390
>
>> sessionInfo()
> R version 2.13.0 (2011-04-13)
> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
>
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
>
> attached base packages:
> [1] stats     graphics  grDevices datasets  utils     methods   base
>
> other attached packages:
> [1] smart.source_1.0     KEGG.db_2.5.0        RSQLite_0.9-4
> [4] DBI_0.2-5            AnnotationDbi_1.14.1 Biobase_2.12.2
>