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I'm using ROntoTools functions to fetch KEGG Graphs and pathway names. There are pathways returned by the function "keggPathwayNames" that are missing from the set of pathways returned by keggPathwayGraphs.
kegg_mmu <- ROntoTools::keggPathwayGraphs(
organism = "mmu", updateCache = TRUE
)
kpn <- ROntoTools::keggPathwayNames(
organism = "mmu", updateCache = TRUE
)
> length(kegg_mmu)
[1] 222
>
> length(kpn)
[1] 343
>
> length(setdiff(names(kpn), names(kegg_mmu)))
[1] 121
>
> setdiff(names(kpn), names(kegg_mmu))[1:10]
[1] "path:mmu00010" "path:mmu00020" "path:mmu00030" "path:mmu00040" "path:mmu00051" "path:mmu00052" "path:mmu00053" "path:mmu00061" "path:mmu00062"
[10] "path:mmu00071"
I'm not whether there is any rhyme or reason to the missing pathways -- for example path:mmu00020 is the citric acid cycle
Any help in obtaining a complete set of pathways would be greatly appreciated.
See below for session info:
> sessionInfo()
R version 4.2.0 (2022-04-22)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Monterey 12.5
Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats4 grid stats graphics grDevices utils datasets methods base
other attached packages:
[1] pheatmap_1.0.12 ggfortify_0.4.14 openxlsx_4.2.5 reticulate_1.25 ggrepel_0.9.1 ggplot2_3.3.6 dplyr_1.0.9
[8] tibble_3.1.7 tidyr_1.2.0 edgeR_3.38.1 limma_3.52.1 org.Mm.eg.db_3.15.0 AnnotationDbi_1.58.0 IRanges_2.30.0
[15] S4Vectors_0.34.0 Biobase_2.56.0 ROntoTools_2.24.0 Rgraphviz_2.40.0 KEGGgraph_1.56.0 KEGGREST_1.36.2 boot_1.3-28
[22] graph_1.74.0 BiocGenerics_0.42.0
loaded via a namespace (and not attached):
[1] httr_1.4.3 pkgload_1.2.4 bit64_4.0.5 jsonlite_1.8.0 splines_4.2.0 here_1.0.1
[7] brio_1.1.3 assertthat_0.2.1 statmod_1.4.36 blob_1.2.3 GenomeInfoDbData_1.2.8 pillar_1.7.0
[13] RSQLite_2.2.14 lattice_0.20-45 glue_1.6.2 RColorBrewer_1.1-3 XVector_0.36.0 colorspace_2.0-3
[19] Matrix_1.4-1 XML_3.99-0.10 pkgconfig_2.0.3 zlibbioc_1.42.0 purrr_0.3.4 scales_1.2.0
[25] generics_0.1.2 ellipsis_0.3.2 cachem_1.0.6 withr_2.5.0 cli_3.3.0 magrittr_2.0.3
[31] crayon_1.5.1 memoise_2.0.1 fansi_1.0.3 tools_4.2.0 lifecycle_1.0.1 stringr_1.4.0
[37] munsell_0.5.0 locfit_1.5-9.5 zip_2.2.0 Biostrings_2.64.0 compiler_4.2.0 GenomeInfoDb_1.32.2
[43] rlang_1.0.2 RCurl_1.98-1.7 rstudioapi_0.13 bitops_1.0-7 testthat_3.1.4 gtable_0.3.0
[49] curl_4.3.2 DBI_1.1.2 R6_2.5.1 gridExtra_2.3 fastmap_1.1.0 bit_4.0.4
[55] utf8_1.2.2 rprojroot_2.0.3 desc_1.4.1 stringi_1.7.6 parallel_4.2.0 Rcpp_1.0.8.3
[61] vctrs_0.4.1 png_0.1-7 tidyselect_1.1.2
One thing I have observed is that for some, but not all, of the missing pathways, the KEGG website does not provide a link to the KGML file. However for other missing pathways, the KGML file is available. For example:
However: Ribosome / path:mmu00020 -- https://www.kegg.jp/pathway/mmu03010 does provide a KGML Download link
On the other hand Biosynthesis of Amino Acids which is also missing, does not offer a KGML download link
Biosynthesis of Amino Acids -- https://www.kegg.jp/pathway/mmu01230
On the third hand, I can access the KGML for Biosynthesis of Amino Acids using KEGGgraph
Another update:
Even though I can download the files for the missing pathways, they don't seem to load correctly
For the ribosome this makes sense, as the "Pathway" does not appear to have edges:
For Biosynthesis of amino acids, it seems like it would make sense to have edges when "non-genes", i.e metabolites, are included.