Last updated: 2019-07-24

Purpose

This protocol describes how to define a query in EPA’s ECOTOX database, for the purpose of extracting data on the LD50 of pesticides to the honey bee, Apis mellifera. Further background on ECOTOX can be found here.

Procedure

Start by going to the ECOTOX Advanced Database Query. Then set the the parameters of the tabs as follows:

  1. Taxonomic
    • Select Kingdom: Animals
    • In the search box, enter apis mellifera
    • In the options for name searches, select Genus/Species Name and Contains
  2. Chemical - use defaults
  3. Test Results
    • Under Endpoints, check LD50
    • Under Effect Measurements, check Mortality Group
  4. Test Conditions
    • Under Test Locations, check Lab
  5. Publications/Updates - use defaults
  6. Report Format
    • In the Report Format box, click the button at the bottom for Edit/View Terrestrial Sort/Displaay
    • Change the Terrestrial Output Selections to include the following data items, which will provide the necessary data and associated metadata for the next step:
      • CAS Number | Chemical Name
      • Chemical Comment
      • Chemical Formulation
      • Dose Number
      • Dose (Author)
      • Doses
      • Effect|Effect Measurement
      • Endpoint
      • Exposure Duration (Days)
      • Exposure Type
      • Exposure Sample Number
      • Observed Response
      • Organism Lifestage
      • Organism Source
      • Reference Citation
      • Reference Number
      • Result Comment
      • Species Common Name
      • Species Scientific Name
      • Test Location
      • Test Method
      • Test Type
    • At the top of the box, sort the data as you prefer
    • Click Finished Editing at the bottom
    • Choose to export in Excel Format
    • Click Perform Query for Terrestrial Data (it may take several minutes to download the results)

Saving the data

Once the query is complete, save the file as a .csv into its permanent location (in this case the directory bee_tox_county/data). Use an informative file name that includes the date the query was performed, e.g. ecotox_ld50_apis_mellifera_YYYYMMDD.csv

Session information

sessionInfo()
R version 3.6.1 (2019-07-05)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.6

Matrix products: default
BLAS:   /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/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] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
 [1] compiler_3.6.1  magrittr_1.5    tools_3.6.1     htmltools_0.3.6
 [5] yaml_2.2.0      Rcpp_1.0.1      stringi_1.4.3   rmarkdown_1.14 
 [9] knitr_1.23      stringr_1.4.0   xfun_0.8        digest_0.6.20  
[13] evaluate_0.14

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