In KEGGREST: Client-side REST access to the Kyoto Encyclopedia of Genes and Genomes (KEGG)

library(knitr)
options(width=80)

hook_output = knit_hooks$get('output')
knit_hooks$set(output = function(x, options) {
  # this hook is used only when the linewidth option is not NULL
  if (!is.null(n <- options$linewidth)) {
    x = knitr:::split_lines(x)
    # any lines wider than n should be wrapped
    if (any(nchar(x) > n)) x = strwrap(x, width = n)
    x = paste(x, collapse = '\n')
  }
  hook_output(x, options)
})

KEGGREST

KEGG is a database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from molecular-level information, especially large-scale molecular datasets generated by genome sequencing and other high-throughput experimental technologies.

KEGGREST allows access to the KEGG REST API. Since KEGG disabled the KEGG SOAP server on December 31, 2012 (which means the KEGGSOAP package will no longer work), KEGGREST serves as a replacement.

The interface to KEGGREST is simpler and in some ways more powerful than KEGGSOAP; however, not all the functionality that was available through the SOAP API has been exposed in the REST API. If and when more functionality is exposed on the server side, this package will be updated to take advantage of it.

Overview

The KEGG REST API is built on some simple operations: info, list, find, get, conv, and link. The corresponding R functions in KEGGREST are: keggInfo(), keggList(), keggFind(), keggGet(), keggConv, and keggLink().

Exploring KEGG Resources with keggList()

KEGG exposes a number of databases. To get an idea of what is available, run listDatabases():

library(KEGGREST)
listDatabases()

You can use these databases in further queries. Note that in many cases you can also use a three-letter KEGG organism code or a "T number" (genome identifier) in the same place you would use one of these database names.

You can obtain the list of organisms available in KEGG with the keggList() function:

org <- keggList("organism")
head(org)

From KEGGREST's point of view, you've just asked KEGG to show you the name of every entry in the "organism" database.

Therefore, the complete list of entities that can be queried with KEGGREST can be obtained as follows:

queryables <- c(listDatabases(), org[,1], org[,2])

You could also ask for every entry in the "hsa" (Homo sapiens) database as follows:

keggList("hsa")

Get specific entries with keggGet()

Once you have a list of specific KEGG identifiers, use keggGet() to get more information about them. Here we look up a human gene and an E. coli O157 gene:

query <- keggGet(c("hsa:10458", "ece:Z5100"))

As expected, this returns two items:

length(query)

Behind the scenes, KEGGREST downloaded and parsed a KEGG flat file, which you can now explore:

names(query[[1]])
query[[1]]$ENTRY
query[[1]]$DBLINKS

keggGet() can also return amino acid sequences as AAStringSet objects (from the Biostrings package):

keggGet(c("hsa:10458", "ece:Z5100"), "aaseq") ## retrieves amino acid sequences

...or DNAStringSet objects if option is ntseq:

keggGet(c("hsa:10458", "ece:Z5100"), "ntseq") ## retrieves nucleotide sequences

keggGet() can also return images:

png <- keggGet("hsa05130", "image") 
t <- tempfile()
library(png)
writePNG(png, t)
if (interactive()) browseURL(t)

NOTE: keggGet() can only return 10 result sets at once (this limitation is on the server side). If you supply more than 10 inputs to keggGet(), KEGGREST will warn that only the first 10 results will be returned.

Search by keywords with keggFind()

You can search for two separate keywords ("shiga" and "toxin" in this case):

head(keggFind("genes", c("shiga", "toxin")))

Or search for the two words together:

head(keggFind("genes", "shiga toxin"))

Search for a chemical formula:

head(keggFind("compound", "C7H10O5", "formula"))

Search for a chemical formula containing "O5" and "C7":

head(keggFind("compound", "O5C7", "formula"))

You can search for compounds with a particular exact mass:

keggFind("compound", 174.05, "exact_mass")

Because we've supplied a number with two decimal digits of precision, KEGG will find all compounds with exact mass between 174.045 and 174.055.

Integer ranges can be used to find compounds by molecular weight:

head(keggFind("compound", 300:310, "mol_weight"))

Convert identifiers with keggConv()

Convert between KEGG identifiers and outside identifiers.

You can either specify fully qualified identifiers:

keggConv("ncbi-proteinid", c("hsa:10458", "ece:Z5100"))

...or get the mapping for an entire species:

head(keggConv("eco", "ncbi-geneid"))

Reversing the arguments does the opposite mapping:

head(keggConv("ncbi-geneid", "eco"))

Link across databases with keggLink()

Most of the KEGGSOAP functions whose names started with "get", for example get.pathways.by.genes(), can be replaced with the keggLink() function. Here we query all pathways for human:

head(keggLink("pathway", "hsa"))

...but you can also specify one or more genes (from multiple species):

keggLink("pathway", c("hsa:10458", "ece:Z5100"))

KEGGREST documentation built on Nov. 25, 2020, 2 a.m.