The Society of Toxicology held its 58th Annual Meeting & ToxExpo March 10-14, 2019 in Baltimore, MD. As part of this meeting, Drs. Ruchir Shah, Deepak Mav, Alex Sedykh, and Juleen Lam presented recent work being done across Sciome’s core competencies: Bioinformatics, Cheminformatics, Literature Review, Data Science and Software Development. Dr. Mav outlined Sciome’s fast and robust workflow for alignment, quantification, and quality control that is tailored to TempO-Seq data; whole transcriptome extrapolation and mechanism of action analysis using GeniE pipeline; and development of a Zebrafish S1500+ sentinel gene set for high throughput transcriptomics. Dr. Lam presented Sciome’s rapid Evidence Mapping (rEM) approach as a way to quickly compile a high-level view of the available evidence using a proof-of-concept case study on the topic of low-calorie sweeteners, and also a case study examining health effects of feminine care products. Dr. Sedykh highlighted work conducted with the National Toxicology Program (NTP) Interagency Center for the Evaluation of Alternative Toxicological Methods (NICEATM) to computationally predict eye irritation and corrosion potential of chemicals as one of the key strategies for animal-free evaluation of ocular toxicity. Dr. Shah led discussions on various topics including:
- Sciome’s approach using deep learning for image analysis of high-throughput toxicology assay images;
- Development of BMDExpress software for benchmark dose (BMD) analysis of toxicogenomic data;
- Sciome’s semi-automated data extraction workbench for supporting systematic review process; which includes more than 20 novel data extraction components of relevance to environmental toxicology created and tested on an annotated dataset from the TACSRIE2018 information extraction challenge.