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Tools to Retrieve relevant AOP information - Holly Mortensen, US Environmental Protection Agency

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This third webinar in the series of Adverse Outcome Pathways (AOPs) was organised on Thursday 30 January 2020. It focused on the core information and telecommunication technologies applications that were built to support AOP development, management and dissemination. Tools and technical tips to facilitate scientific knowledge assembling and evaluations were also presented. The AOP framework implements a collaborative and innovative approach for collecting mechanistic knowledge from various sources that can eventually support chemical safety assessment. Holly Mortensen from the US Environmental Protection Agency presented ways of retrieving information from databases and other AOP tools.

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Tools to Retrieve relevant AOP information - Holly Mortensen, US Environmental Protection Agency

  1. 1. TOOLSTO RETRIEVE RELEVANT AOP INFORMATION Holly M. Mortensen, US EPA Center for Public Health and Environmental Assessment, RTP, NC, USA January 30, 2020 ChemAOP Lit Tools AOP-helpFinder
  2. 2. • ChemAOP Lit Tools – MESH based lit search tools (Nancy Baker, US EPA) • AOP-helpFinder – Text-mining and graph theory applied to link KEs with AOP stressors (Karine Audouze, Université de Paris) • AOPXplorer – Cytoscape plug-in based on the AOPOntology (Lyle Burgoon, US Army Corp) • AOPERA – 3rd party tool identifier to link chemicals to AOPs (Taylor Rycroft, US Army Corp) • AOP-DB – AOP profiling tool for AOPs from the AOP-Wiki (Holly Mortensen, US EPA) Tools for AOP Users
  3. 3. Input: AOP of interest Output: Chemical stressors ChemAOPConnect mines lit to find associations between KE and AOP The ChemAOPConnect tools are currently available for 8 AOPs at ftp://newftp.epa.gov/COMPTOX/Sustainable_Chemistry_Data/aop/ Chem-AOP Lit tools: ChemAOPConnect
  4. 4. Chem-AOP Lit tools: PubMed Abstract Sifter https://epa.figshare.com/articles/PubMed_Abstract_Sifter/10324379 ftp://newftp.epa.gov/COMPTOX/Sustainable_Chemistry_Data/Chemistry_Dashboard/Abstract_ Sifter/AbstractSifter.zip • Input: Chemical list • Output: Lit links to KE or AO
  5. 5. The AOP-helpFinder tool Karine Audouze karine.audouze@univ-paris-diderot.fr Applications with bisphenols: Carvaillo et al., 2019 https://doi.org/10.1289/EHP4200 Rugard et al., 2019 https://doi.org/10.1093/toxsci/kfz214 Stressors Biological events AOP network hypothesis Text mining Systems tox. Curation
  6. 6. With AOPXplorer you can: - Visualize AOPs from the AOP Ontology - AOP Ontology is a community resource updated with AOPs from the AOP-Wiki and disease pathway information - Perform data analysis in R - Overlay your data with Cytoscape AOPXplorer is looking for new community submissions! 2 routes for submission • Github pull request (clone the repository, add your AOPN as a cytoscape file, make a pull request) https://github.com/DataSciBurgoon/a op_networks • Email Lyle Burgoon (lyle.d.burgoon@erdc.dren.mil)
  7. 7. Identify tools to link chemicals to AOPs https://igbb.github.io/AOPERA_HTML/#welcome Rycroft et al, ALTEX 2019 Links to publicly available tools, based on four levels of information needed: Step1 INPUT: Uncharacterized Chemical; OUTPUT: six tools to help find MIEs, KEs, or AOs. Step 2: INPUT: Chemical with outcome, no mechanism; OUTPUT: 10 tools to identify chemical analogs Step 3: INPUT: Chemical with some information; OUTPUT: six tools to help find MIEs, KEs, or AOs. Step 4: INPUT: Chemical with single MIE, no biol context; OUTPUT: two tools that identify AOPs from Ste
  8. 8. xml INPUT: AOP Wiki ID , Entrez/Hugo Gene ID, AOP Stressor Available Online Summer 2020!
  9. 9. Basic Search
  10. 10. Batch Download
  11. 11. • We are very grateful for your feedback! • Please send questions to: Nathalie.DELRUE@oecd.org Feedback? Questions?

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