CvTdb is a database with chemical toxicokinetic data. This post will show you how to use the CvTdb in R with BioBricks.

First, install biobricks:

bash 
pip install biobricks
biobricks configure # follow the prompts

Go to docs.biobricks.ai to learn more about the biobricks package.

Then, install the cvtdb asset:

bash 
biobricks install cvtdb
biobricks assets cvtdb 
# cvtdb_sqlite: .../brick/cvtdb.sqlite

The assets function tells us the path of the sqlite file this asset distributes.

Load the cvtdb sqlite file in R:

r 
library(biobricks)
library(tidyverse)
library(RSQLite)
cvtdb_assets <- biobricks::bbassets("cvtdb")
cvtdb <- dbConnect(RSQLite::SQLite(), cvtdb_assets$cvtdb_sqlite)
RSQLite::dbListTables(cvtdb)
# [1] "chemicals"        "conc_time_values" "documents"        "series"          
# [5] "studies"          "subjects"         "tk_parameters"

We can see that there are 7 tables in the database.

Click below to see the database schema:

cvtdb
Installing cvtdb is as simple as `biobricks install cvtdb`. The schema is pretty simple, with the tk_parameters table holding the key toxicokinetic parameters

There are 1816 rows in the tk_parameters table which references 756 measured AUC parameters. Let’s make an AUC table that references a chemical, it’s AUC value, and the study from which that came:

r 
chemicals <- tbl(cvtdb, "chemicals") |> collect() |> 
    select(chemical_id = id, dsstox = dsstox_substance_id)

series <- tbl(cvtdb,"series") |> collect() |> 
    select(series_id = id, chemical_id = fk_analyzed_chemical_id) |> 
    inner_join(chemicals,by="chemical_id") |> distinct()

dsstox_auc <- tbl(cvtdb, "tk_parameters") |> 
    filter(parameter_name=="AUC") |> collect() |>
    mutate(value = as.numeric(parameter_value)) |>
    inner_join(series,by=c("fk_series_id"="series_id")) |>
    select(dsstox,value)

dsstox_auc
# # A tibble: 692 × 2
#    dsstox           value
#  1 DTXSID3061635    1061.
#  2 DTXSID6044519    1855.
#  3 DTXSID20873970  24276

This is the key data in the cvtdb database. There are a few issues in the cvt database right now (see issue) but I’m sure they will be resolved soon.