U.S. Environmental Protection Agency Office of Research and Development Building an Adverse Outcome Pathway Framework through HTS Data and Literature Mining Integration Nancy C. Baker1, Nisha S. Sipes2, M. Shane Hutson3, Thomas B. Knudsen2 1Lockheed Martin, RTP, NC, 2U.S. EPA, ORD, National Center for Computational Toxicology, 3Departments of Physics and Biological Sciences, Vanderbilt University, Nashville, TN Footnotes Go Here Footnotes Go Here Footnotes Go Here Footnotes Go Here Footnotes Go Here Footnotes Go Here Footnotes Go Here Footnotes Go Here Footnotes Go Here Footnotes Go Here Footnotes Go Here Overview Literature Data Nancy Baker l baker.nancy@epa.gov l 919-541-2680 Interpreting EPA’s ToxCast in vitro assay data in the context of Adverse Outcome Pathway (AOP) development is a significant challenge. While chemical activation in these assays may shed light on the molecular initiating event, it can be difficult to identify the downstream effect of these activities at higher levels of biological organization (e.g., cellular, tissue, organ) that could potentially lead to a toxicity endpoint. In this research, we explore applications of literature mining techniques that can be readily used to build and evaluate an AOP framework from in vitro data. We use cleft palate as a prototype and focus on the ToxCast assay targets that were found to have a significant univariate association with cleft palate / cleft lip (CLP) in ToxRefDB and the literature. DISCLAIMER: does not reflect EPA policy Proteins Chemicals Effects 51 million annotations 24 million annotations 18 million annotations >22 million articles A connection Analyze the EPA’s ToxCast HTS dataset containing > 1,000 unique chemicals tested across >500 in vitro assays to identify the assays with the most significant univariate association with chemicals that cause cleft palate or cleft lip. Find the literature connections between ToxCast targets and cell-level activity/entities and tissue-level activity and entities. Connections are defined as an article co-annotation between a target protein and the cell/tissue entity. Strategy Target Tissue Level CLP Organ Cell Level Option 1. Binary relationships Option 2. Expand relationships Option 3. Bidirectional relationships Results Target Tissue Level CLP Organ Cell Level ToxCast: 56 chemicals in the ToxCast libraries were identified as CLP actives by reviewing data in ToxRefDB and the biomedical literature. A statistical analysis of the assay data identified 29 assays that correlated significantly with the CLP endpoints. (Student’s T-test (p<=0.05)) A subset of those assays with the corresponding Medical Subject Heading (MeSH) term for the target protein is found in Table 1. These statistical correlations represent potential molecular targets that have been assayed in the ToxCast portfolio and serve as a potential entry point for AOPs leading to a cleft palate/cleft lip phenotype in pregnant rats and/or rabbits. Literature: The search of EPA’s biomedical literature database using the term Cleft Palate retrieved 36 unique tissue MeSH terms, 37 cell types, 34 cellular processes, and 54 non-cellular processes. Co-annotations of these tissue or cell types and any of the MeSH terms for the ToxCast targets (Table 1) were also retrieved. The articles were counted and the results output to the database and extracted (with hyperlinks) into the spreadsheets show below. Observations deduced from the subject categories serve as a starting point to fill in the biological space between the assays and the endpoint based on what is known in the literature. Target Cell Level Tissue Level Tissue Level Tissue Level Tissue Level CLP Organ CLP Organ CLP Organ Organ CLP Organ CLP Organ Organ AOP Framework: Table 1. Selected assays with significant univariate association with cleft lip / cleft palate; Blue: nuclear receptors; Gray: GPCRs; Green: other ToxCast Assay Target - selected MeSH term NVS_ENZ_oCOX1 Cyclooxygenase 1 NVS_ENZ_hElastase Leukoc