vignettes/substance-info.Rmd
substance-info.RmdThis vignette describes several use cases for retrieving substance information from zinc15.docking.org using the Zr R package.
To follow along, make sure Zr package is installed
install.packages("devtools")
devtools::install_github("MaomLab/Zr")And familiarize yourself with with http://zinc15.docking.org
Tanaka et al., (2015, 10.1371/journal.pone.0135657) observe uremic solutes that accumulate when the kidneys fail. In Supplementary table 2, they list the 120 uremic compounds they observe. Here are the ones with HMDB Ids:
uremic_solutes <- c("HMDB00001", "HMDB00017", "HMDB00020")To retrieve information about these compounds we can use Zr package
##
## Attaching package: 'dplyr'## The following objects are masked from 'package:stats':
##
## filter, lag## The following objects are masked from 'package:base':
##
## intersect, setdiff, setequal, union
s_info <- search_for_substances(uremic_solutes, verbose=T)## making request:
## url: http://zinc15.docking.org/substances/search?count=all
## making request:
## url: http://zinc15.docking.org/substances/search?count=all
## making request:
## url: http://zinc15.docking.org/substances/search?count=all
s_info %>% str## 'data.frame': 3 obs. of 11 variables:
## $ search_term : chr "HMDB00001" "HMDB00017" "HMDB00020"
## $ zinc_id : chr "ZINC000002563973" "ZINC000000120316" "ZINC000000213065"
## $ preferred_name : chr "4-methyl-histidine" "4-pyridoxate" "4-hydroxyphenylacetate"
## $ smiles : chr "Cn1cnc(C[C@H](N)C(=O)O)c1" "Cc1ncc(CO)c(C(=O)O)c1O" "O=C(O)Cc1ccc(O)cc1"
## $ purchasability : chr "In-Stock" "In-Stock" "In-Stock"
## $ features : chr "set(['in-man', 'endogenous'])" "set(['in-man', 'endogenous'])" "set(['world', 'endogenous'])"
## $ aggregator : logi FALSE FALSE FALSE
## $ drug_code : num 213 213 211
## $ drug_level : chr "in-man" "in-man" "world"
## $ biological_code : num 203 203 203
## $ biological_level: chr "endogenous" "endogenous" "endogenous"