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Ecotoxicology Knowledgebase ECOTOXicology Knowledgebase: Modernizing the Literature Review and Data Curation Processes, and Mapping Ecological Toxicity of Per- and Polyfluoroalkyl Substances (PFAS) Jennifer OlkerPhoto, image Postdoctoral area measures 2” H x 6.93” W and can be Researchermasked by a collage strip of one, two or three images. Colleen ElonenThe photo, imageECOTOX area is located 3.19” from coordinator left and 3.81” from top of page. Each image used in collage should be reduced or cropped to a maximum of 2” high, stroked with a 1.5 pt white frame and positioned edge-to-edge with accompanying images. US EPA ECOTOX Project Team: Colleen Elonen Jennifer Olker GDIT contract staff Dale Hoff SEE staff Rong-Lin Wang Office of Research and Development www.epa.gov/ecotox Overview • Background and History for ECOTOX Knowledgebase • Modernizing the ECOTOX Pipeline (C. Elonen, SOT 2020) • Mapping ecological toxicity of PFAS with ECOTOX Protocols (J. Olker, SOT 2020) 2 What is the ECOTOX Knowledgebase? Publicly available, curated database providing toxicity data from single-chemical exposure studies to aquatic life, terrestrial plants, and wildlife • From comprehensive search and review of open and grey literature – Data extracted from acceptable studies, with up to 250 fields – Updated quarterly • 30+ year history: www.epa.gov/ecotox/ Originated in the early 1980s, US Environmental Protection Agency Office of Research and Development 3 Who uses the ECOTOX Knowledgebase? Clients Contacting ECOTOX Support line 2005 - 2016 (n = 2813) US EPA Headquarters Local Govt. International Govt. 4% 1% 8% Govt. Contractors 25% US EPA Regional Office 4% Unknown 5% University/Academia Other Federal 6% Agencies 4% US EPA Laboratory 4% State Govt. 7% Private Sector ~8000 Distinct hosts/month 32% 4 Program Offices & Regions Applications: use in environmental decision making Used for every Ambient Water Quality Criteria for Aquatic Life since 1985. Used for every Ecological Risk Assessment for Office of Pesticides for chemical registration and re-registration (FY19 – 30 chemicals). Used by OLEM (Superfund and RCRA), HQ, Regions and States for site assessments and in emergency response Providing ecological hazard data for the prioritization and assessment of chemicals for TSCA/Lautenberg Act Providing ecological toxicity data for PFAS to researchers, EPA ERA Forum, DoD Tri-Services ERA Work Group, and others 5 Applications of ECOTOX ECOTOX Knowledgebase Chemical EPA Program Offices and Regions, environmental States, Tribes, Other Federal Agencies toxicity data for and International Entities aquatic life, Ecological Risk Assessments terrestrial plants Ambient Water Quality Criteria and wildlife Ecological Screening Values Chemical Prioritization Emergency Response Tools and Applications Species Sensitivity Distributions (e.g., US EPA’s WebICE, NOAA’s CAFÉ) PNECs and threshold values (e.g., EcoTTC) QSAR (e.g., ECOSAR, TEST, OECD QSAR Toolbox) BCF modeling and validation Chemicals SeqAPASS HERO Adverse Outcome Pathway (AOP) development Dashboard (Health & Environmental Research Online) Interoperability Interoperability with databases/tools 6 ECOTOX Pipeline: Systematic Review/Data Curation Chemical verification Chemical-based Search Terms: Sources include: • Chemical name and CASRN • STN and development of • Synonyms, tradenames • Pesticide Action Network (PAN) search terms • Other relevant forms (metabolites, degradants, • EPA’s Pesticide Fate Database (PFATE) parent compound, related chemicals) • EPA’s Chemistry Dashboard. Literature search: Use chemical-specific search terms to query multiple literature search engines Citations from: ProQuest/ Science ToxNet Dissertation Agricola Current Contents Already in CSA Direct Abstracts (WoS) Unify* Conduct literature n = 5,631 11,178 317 234 4,861 15,347 333 Identification searches *Internal USEPA ECOTOX database ~37,000 citations downloaded Initial removal of duplicates Not applicable (excluded): n = 8,265 references Identify and acquire Title and Abstract Screening Chem Methods: 3,462 No Toxicant: 221 potentially applicable n = 8,653 references Human Health: 1,797 Duplicate: 153 False Hit: 1,333 Review: 50 studies Fate: 510 Mixture: 12 Screening Survey: 287 Other: 121 Bacteria: 233 Review literature for For Review (Full Text Screening) No PFAS in reference: n = 85 references applicability to n = 388 references Did not meet acceptability criteria (excluded): ECOTOX n = 142 references Eligibility Awaiting Review and Data Extraction Data Extracted from Acceptable n = 1 references Extract data into Papers ECOTOX n = 245 references with 7,496 total records Included Knowledgebase 7 ECOTOX Pipeline: Systematic Review/Data Curation Chemical verification Chemical-based Search Terms: Sources include: • Chemical name and CASRN • STN and development of • Synonyms, tradenames • Pesticide Action Network (PAN) search terms • Other relevant forms (metabolites, degradants, • EPA’s Pesticide Fate Database (PFATE) parent compound, related chemicals) • EPA’s Chemistry Dashboard. Literature search: Use chemical-specific search terms to query multiple literature search engines Citations from: ProQuest/ Science ToxNet Dissertation Agricola Current Contents Already in CSA Direct Abstracts (WoS) Unify* Conduct literature n = 5,631 11,178 317 234 4,861 15,347 333 Identification searches *Internal USEPA ECOTOX database ~37,000 citations downloaded Initial removal of duplicates Not applicable (excluded): n = 8,265 references Identify and acquire Title and Abstract Screening Chem Methods: 3,462 No Toxicant: 221 potentially applicable n = 8,653 references Human Health: 1,797 Duplicate: 153 False Hit: 1,333 Review: 50 studies Fate: 510 Mixture: 12 Screening Survey: 287 Other: 121 Bacteria: 233 Review literature for For Review (Full Text Screening) No PFAS in reference: n = 85 references applicability to n = 388 references Did not meet acceptability criteria (excluded): ECOTOX n = 142 references Eligibility Data Extracted from Acceptable Papers Awaiting Review and Data Extraction Data extraction n = 245 references with 7,496 total records n = 1 references Study quality Data from High Quality Studies Included evaluation n = ___ references 8 Identify, Test, and QA Search Terms Chemical verification Search various sources for chemical terms, and development of Synonyms, verify CAS, eliminate poor search terms search terms Tak(Acilid OR Albrass OR Bexton OR "CP 31393" OR "Kartex A" OR Muharicid OR Niticid OR Propachlor OR Propachlore OR Ramrod OR Satecid OR "US EPA PC Code 019101") Conduct literature Identification searches Identify and acquire Couple hour process potentially applicable studies Screening Review literature for applicability to ECOTOX Eligibility Enter chemical terms Data extraction into template for Study quality abstracting databases Included evaluation 9 Identify, Test, and QA Search Terms Chemical verification Web-based tool to identify and document and development of relevant search terms search terms Tak(Acilid OR Albrass OR Bexton OR "CP 31393" OR "Kartex A" OR Muharicid OR Niticid OR Propachlor OR Propachlore OR Ramrod OR Satecid OR "US EPA PC Code 019101") AND NOT key(human* or child* or occupat* OR infant* OR Conduct literature homind* OR woman OR women OR patient* OR OSHA OR Identification chromatograph* OR Spectrometr* OR pediatric*) searches Identify and acquire Couple hour process potentially applicable studies Screening Review literature for applicability to ECOTOX Eligibility Chemical terms Data extraction automatically formatted for abstracting databases Study quality Included evaluation 10 ECOTOX Literature Searches Search Engines Chemical verification Chemical specific searches 1. Science Direct and development of (using terms from chemical verification step) 2. AGRICOLA search terms OR 3. TOXNET 4. ProQuest ESPM Monthly electronic searches 5. ProQuest Dissertation of 11 highly relevant journals Abstracts 6. Web of Science/ Conduct literature Current Contents Identification searches Identify and acquire potentially applicable studies Screening Review literature for applicability to ECOTOX In 2019: 159,727 Eligibility references were manually skimmed Data extraction for applicability Study quality Included Collate data and remove duplicates evaluation 11 ECOTOX Literature Searches Excel-based tool Search Engines Chemical verification 1. Science Direct and development of (Abstract-Sifter Plus) to 2. AGRICOLA search terms search multiple sources 3. TOXNET 4. ProQuest ESPM 5. ProQuest Dissertation Abstracts 6. Web of Science/ Conduct literature Current Contents Identification searches Identify and acquire potentially applicable studies Screening Review literature for applicability to ECOTOX References can be Eligibility ‘sifted’, reviewed, or exported as .ris Data extraction Study quality Included Collate data and remove duplicates evaluation 12 Skimming for Applicability: Chemical verification Title and Abstract and development of search terms Conduct literature Identification searches Skim titles and Identify and acquire abstracts, use exclusion potentially applicable criteria to eliminate studies Screening non-applicable Review literature for applicability to ECOTOX Eligibility Data extraction Send applicable reference Study quality list for acquisition Included evaluation 13 Skimming for Applicability: Chemical verification Title and Abstract and development of Partnering with NTP/SCIOME to develop language search terms learning tool for skimming/prioritizing abstracts Conduct literature Identification searches Skim titles
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