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 ------- |