data dictionary?

[tcrombie]

Hi there,

I'm interested in pulling out all the dose response fit parameters in the toxcast database for a set of 21 chemicals. My issue is that I can't find a complete data dictionary anywhere for the level 5 multiple comparison (mc5) variables returned by my query.

Can anyone help me define all the variables returned from my query? (see list of variables below)

For example, I think that modl_ga = The log10AC50 for the best fit model, based on Appendix B at the bottom of this vignette, but I'm not sure what all the other modl_<other stuff here> variables are.

Workflow

1. Installed MySQL
2. Built the database locally using the mysql_th813_prod_internal_invitrodb_v3_5_2022-07-20_00h00m.dmp file.
3. Installed the tcpl and tcplfit2 packages in R v(4.2.1)
4. Used the tcplConf function to setup queries to the database
5. Ran the code below to query the invitrodb_v2 database

library(tidyverse)
library(tcplfit2)
library(tcpl)

# define chemical list by CAS
chems <- c("94-75-7", "116-06-3", "1912-24-9", "10108-64-2", "63-25-2",
          "5234-68-4", "2921-88-2",	"8018-01-7", "16752-77-5", "115-09-3",
          "7718-54-9", "1910-42-5", "114-26-1", "175013-18-0", "115-86-6",
          "7646-85-7", "121-75-5", "122453-73-0", "1327-53-3", "1897-45-6",
          "7447-39-4")

# get every endpoint ID in the database: aeid = (assay endpoint ID)
aeids <- tcplLoadAeid()

# pull all the mc5 data for every endpoint ID?
mc5 <- tcplPrepOtpt(
  tcplLoadData(lvl=5, # data level
               fld="aeid", # query on assay endpoint ID
               val=aeids$aeid, # give me every value
               type = "mc") # return multiple concentration data type
)

# filter to the chemicals I care about, sorry everybody else, lol
mc5.chem <- mc5 %>%
  dplyr::filter(casn %in% chems)

# glimpse the data to see output
glimpse(mc5.chem)

6. Got the mc5.chem data.frame = mc5.chem.issue.rda in issue_files.zip
7. I've been building the data dictionary for this object but I don't knwo what the variables are with question marks in the dd.csv file in issue_files.zip
   Here's the zip file issue_files.zip

Major variables in question - what are these bad boys?

modl_er
modl_tp
modl_ga
modl_gw
modl_la
modl_lw
modl_rmse
modl_prob
modl_acc
modl_acb
modl_ac10

[brown-jason]

Check out page 8 of the data release summary pdf
https://clowder.edap-cluster.com/files/62fa82fee4b055edffc39680?dataset=62c435afe4b01d27e3b2b603&space=62bb560ee4b07abf29f88fef

We also have a few vignettes on cran that might help if you need more information about methodology.

[tcrombie]

Thanks @brown-jason, the data release summary was exactly what I needed. I probably should have thought to read the README 😄

[brown-jason]

Sounds good, moving to discussions in case anyone else has this issue in the future.