United States
Environmental Protection
Agency

ECOTOX Knowledgebase Virtual Training

Breakout Group Worksheet: Beginner

This worksheet was developed for the Breakout Group session of the ECOTOX Knowledgebase Virtual
Training, hosted by the U.S. Environmental Protection Agency's Center for Computational Toxicology
and Exposure on February 7, 2023.

For more information about the ECOTOX Knowledgebase tool:

•	Visit the ECOTOX Knowledgebase at www.epa.gov/ecotox.

•	Contact ECOTOX support at ecotox.support@epa.gov or by calling 218-529-5225.

•	Read more in Olker et al. 2022, https://doi.org/10.10Q2/etc.5324.

Goal

Use the ECOTOX knowledgebase to identify and explore records available for specific chemicals, species
groups, and other refined searches.

1. Find the chemical information for DEET from the list provided on page 5 of this worksheet.
[Note: For the first round of this worksheet, we will all start with the chemical DEET. If you have
time during or after the training, select another chemical from page 5 to work through on the
worksheet]

a. Type the chemical and its CAS Registry Number in the space below.

2. Because we are starting with a chemical and have no other parameters, should you start with
Search or Explore?

3. Create a Custom Group for your chemical. [Hint: Go to Explore, select Chemicals, then create
custom group. Enter in your chemical name or CAS number. Then refer to the list of Query Filters
on the left-hand side to walk through the next set of questions.]

a. How many Species Groups have records in ECOTOX for the selected compound(s)?

Directions

l


-------
United States
Environmental Protection
Agency

4. Refine these results by selecting the Fish Species Group. [Note: For the first round of this

worksheet, we will all start with Fish. If you have time during or after the training, select another
species group from page 5 to work through on the worksheet.]

a. Based on the Species Group you selected, take note that the "Aquatic"/"Terrestrial"
options at the top of the left-hand side may change automatically depending on which
Species Group(s) are selected. For example, Birds only have Terrestrial data. You can
also manually change these selections to narrow results, for example if you only want
Terrestrial data for Amphibians (which could have both Aquatic and Terrestrial data).
What changed when you selected the Fish Species Group? If you are using another
species group that has both habitats, select a specific habitat.

5. Change the view as needed (i.e., Group Summary, Records, Plot View) to answer the following
questions:

a. Change your results to Records view.

i. What types of effects were measured in the Species Group you focused on?
[Hint: Your answer should include everything—even where no effect was
measured (e.g., NOEC)!]

ii. What specific effects were observed in the Species Group you focused on?
What were some specific measured effects? [Hint: This answer includes only
those where there was an effect (i.e., LOEC, LC50, etc.).]

b. Change your results to Plot View.

i. What were the lowest concentrations for which these effects were reported?

ii. What paper or papers were these lowest concentrations reported in? Copy the
citation information (including the ECOREF number) by clicking on the Author(s)
name in the reference column.

iii. Write down the ECOREF number (identifier for the reference).

2


-------
United States
Environmental Protection
Agency

c. Select Send Query Filters to Search at the top of the right-hand side. This will open
Search in a new tab. [Hint: Be sure to click the green Update Search button on the
bottom-left!]

i. Modify the Publications Options to limit the output to the reference identified
above. How many records are displayed?

ii. Use the Customize Output Fields feature to add fields to the output table. Select
Control and any other output fields of interest (e.g., Gender, Experimental
Design, and EE Comment). What did you choose?

iii. Did the authors of the above paper(s) report what types of controls were used?
If so, what were the types of controls?

iv. Were you able to find/access the publication to read/review the original results?
Did you encounter challenges or have questions about the results?

d. Expand the Publications Options to include all references that meet the search
parameters (no longer limiting results to the single identified reference). Now how
many records are displayed?

e. Export and save the results as an Excel file and filter them to show the records from the
reference with the lowest effect concentrations discussed in the previous steps. Now,
try to find the same list of papers by using the Search module. Begin by adding the
chemical name or CAS Registry Number and species group to the parameters on the
left-hand side.

i. Did you find that Explore or Search was an easier starting point for your query?
List one example of why.

3


-------
United States
Environmental Protection
Agency

Reflection

1. In what case example from your work environment would ECOTOX be useful?

2. What have you learned about the process and workflow used to find information and papers in
ECOTOX?

3. What challenges did you encounter, and how did you solve them?

4


-------
*>EPA

United States
Environmental Protection
Agency

/C?s

fA/owv.^0

Chemical List

Category

Compound(s)

Full Chemical Name

CAS Registry
Number(s)

Pesticide/Herbicide

Atrazine

6-Chloro-N-ethyl-N'-(l-
methylethyl)-l,3,5-triazine-
2,4-diamine

1912-24-9

Pesticide/Herbicide

Roundup

N-

(Phosphonomethyl)glycine
compd. with 2-propanamine
(1:1)

38641-94-0

Pesticide/Herbicide

Chlorpyrifos

Phosphorothioic acid, 0,0-
Diethyl 0-(3,5,6-trichloro-2-
pyridinyl) ester

2921-88-2

Metal

Cadmium



7440-43-9, 10108-
64-2, plus
11 others in the
Cadmium group

Metal

Lead



7439-92-1, 7758-
95-4, 301-04-2,
10099-74-8, plus 9
others in the Lead
group

Metal

Selenium



35 unique
compounds in the
Selenium group

Pharmaceutical/Personal

17a-

(17alpha)-19-Norpregna-

57-63-6

Care Product

Ethinylestradiol

l,3,5(10)-trien-20-yne-3,17-
diol



Pharmaceutical/Personal

Clofibrate/Clofibric

2-(4-Chlorophenoxy)-2-

637-07-0, 882-09-7

Care Product

Acid

methylpropanoic acid, Ethyl
ester; 2-(4-Chlorophenoxy)-
2-methylpropanoic acid



Pharmaceutical/Personal

DEET

N, N-Diethyl-meta-

134-62-3

Care Product



toluamide or
diethyltoluamide



Species Groups

Vertebrates

Invertebrates

Plants and Other

Fish

Insects/Spiders

Flowers, Trees, Shrubs, Ferns

Mammals

Worms

Algae

Birds

Molluscs

Fungi

Amphibian

Crustaceans

Moss, Hornworts

Reptiles

Other Invertebrates

Miscellaneous (Communities, Higher Taxonomic Level)

5


-------
United States
Environmental Protection
Agency

ECOTOX Knowledgebase Virtual Training

Breakout Group Worksheet: Beginner ANSWERS

This worksheet was developed for the Breakout Group session of the ECOTOX Knowledgebase Virtual
Training, hosted by the U.S. Environmental Protection Agency's Center for Computational Toxicology
and Exposure on February 7, 2023.

For more information about the ECOTOX Knowledgebase tool:

•	Visit the ECOTOX Knowledgebase at www.epa.gov/ecotox.

•	Contact ECOTOX support at ecotox.supportffiepa.gov or by calling 218-529-5225.

•	Read more in Olker et al. 2022. https://doi.org/10.10Q2/etc.5324.

Use the ECOTOX knowledgebase to identify and explore records available for specific chemicals, species
groups, and other refined searches.

1. Find the chemical information for DEET from the list provided on page 5 of this worksheet.
[Note: For the first round of this worksheet, we will all start with the chemical DEET. If you have
time during or after the training, select another chemical from page 5 to work through on the
worksheet]

a. Type the chemical and its CAS Registry Number in the space below.

2. Because we are starting with a chemical and have no other parameters, should you start with
Search or Explore?

3. Create a Custom Group for your chemical. [Hint: Go to Explore, select Chemicals, then create
custom group. Enter in your chemical name or CAS Registry Number. Then refer to the list of
Query Filters on the left-hand side to walk through the next set of questions.]

a. How many Species Groups have records in ECOTOX for the selected compound(s)?

Goal

Directions

DEET/diethyltoluamide, 134-62-3

Explore

6 species groups: algae, fish, crustaceans, insects, worms, birds

1


-------
*>EPA

United States
Environmental Protection
Agency

/C?s

fA/owv.^0

4.	Refine these results by selecting the Fish Species Group. [Note: For the first round of this
worksheet, we will all start with Fish. If you have time during or after the training, select another
species group from page 5 to work through on the worksheet]

a. Based on the Species Group you selected, take note that the "Aquatic"/"Terrestrial"
options at the top of the left-hand side may change automatically depending on which
Species Group(s) are selected. For example, Birds only have Terrestrial data. You can
also manually change these selections to narrow results, for example if you only want
Terrestrial data for Amphibians (which could have both Aquatic and Terrestrial data).
What changed when you selected the Fish Species Group? If you are using another
species group that has both habitats, select a specific habitat.

Only Aquatic is now selected.

5.	Change the view as needed (i.e., Group Summary, Records, Plot View) to answer the following
questions:

a. Change your results to Records view.

i.	What types of effects were measured in the Species Group you focused on?
[Hint: Your answer should include everything—even where no effect was
measured (e.g., NOEC)!]

Biochemistry, Genetics, Growth, Morphology, Mortality, Multiple
[Additional guidance: Look in effect column or go to Effect Groups in sidebar.]

ii.	What types of effects were observed in the Species Group you focused on?
What were some measured effects? [Hint: This answer includes only those
where there was an effect (i.e., LOEC, LC50, etc.).]

3 Effect Groups (Genetics, Morphology, and Mortality)

3 specific Effect Measurements: Androgen receptor mRNA, Organ weight in
relationship to body weight, Mortality

b. Change your results to Plot View.

i.	What were the lowest concentrations for which these effects were reported?

0.0006 mg/L, which can be found from the plot or the list below the plot.

[Additional guidance: Another way to find this answer is by creating a Custom
Plot and changing the Category Legend to "Endpoint." You can then deselect
(i.e., turn off) the NOEC points to see the other endpoints.]

ii.	What paper or papers were these lowest concentrations reported in? Copy the
citation information (including the ECOREF number) by clicking on the Author(s)
name in the reference column.

Zenobio, J.E., B.C. Sanchez, L.C. Archuleta, and M.S. Sepulveda. Effects of
Triclocarban, N,N-Diethyl-meta-Toluamide, and a Mixture of Pharmaceuticals

2


-------
United States
Environmental Protection
Agency

and Personal Care Products on Fathead Minnows (Pimephales promelas).
Environ. Toxicol. Chem.33(4): 910-919, 2014.

iii. Write down the ECOREF number (identifier for the reference).

ECOREF #168459

c. Select Send Query Filters to Search at the top of the right-hand side. This will open
Search in a new tab. [Hint: Be sure to click the green Update Search button on the
bottom-left!]

i. Modify the Publications Options to limit the output to the reference identified

ii.	Use the Customize Output Fields feature to add fields to the output table. Select
Control and any other output fields of interest (e.g., Gender, Experimental
Design, and EE Comment). What did you choose?

User defined selections.

iii.	Did the authors of the above paper(s) report what types of controls were used?
If so, what were the types of controls?

Yes, Carrier or solvent.

iv.	Were you able to find/access the publication to read/review the original results?
Did you encounter challenges or have questions about the results?

[Open response]

d. Expand the Publications Options to include all references that meet the search
parameters (no longer limiting results to the single identified reference). Now how
many records are displayed?

[Additional guidance: To do this, go to Publication Options and delete the reference
number.]

[Note: If you use the Reset button in Publication Options and it does not work or causes
it to "break/' you can delete reference number or click in the Ref Num(s) field and hit
backspace. This should trigger the green "Update Search" button to reappear. The
ECOTOX team is aware of this issue.]

above. How many records are displayed?

2

7

3


-------
United States
Environmental Protection
Agency

e. Export and save the results as an Excel file and filter them to show the records from the
reference with the lowest effect concentrations discussed in the previous steps. Now,
try to find the same list of papers by using the Search module. Begin by adding the
chemical name or CAS Registry Number and species group to the parameters on the
left-hand side.

i. Did you find that Explore or Search was an easier starting point for your query?

List one example of why.

Reflection

1. In what case example from your work environment would ECOTOX be useful?
[Open response]

2. What have you learned about the process and workflow used to find information and papers in
ECOTOX?

[Open response]

3. What challenges did you encounter, and how did you solve them?
[Open response]

[Open response + example]

4


-------