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SeqAPASS implements strategic connections of knowledge streams to inform species extrapolation for chemical safety
Citation:
LaLone, C. SeqAPASS implements strategic connections of knowledge streams to inform species extrapolation for chemical safety. SETAC North America, Pittsburgh, PA, November 13 - 17, 2022. https://doi.org/10.23645/epacomptox.21561186
Impact/Purpose:
Presentation to the Society of Environmental Toxicology and Chemistry (SETAC) annual meeting November 2022. Interoperability is being considered throughout the development and design of new toxicology tools and databases to ensure relevant and related information useful to researchers and decision-makers can be applied to chemical safety evaluations and environmental management practices. This presentation describes the importance of linking appropriate information to the Sequence Alignment to Predict Across Species Susceptibility (SeqAPASS) tool for the ability to rapidly and systematically explore scientific questions surrounding species extrapolation and synthesize results for both research and decision-makers.
Description:
No one tool or methodology can provide all necessary information regarding the impacts of a chemical to a species, let alone to the diversity of species. Transparent, scientifically supported development of tools that strategically connect to one another to fulfill data and knowledge needs for decision-making are promising for replacing and complementing toxicity testing. Therefore, throughout the tool development process, interoperability and connectivity to the correct resources is critical. The Sequence Alignment to Predict Across Species Susceptibility (SeqAPASS) tool was created to bring together tools and databases for the purpose of informing challenges in species extrapolation relevant to researchers and decision-makers concerned with chemical safety. The SeqAPASS tool specifically compares protein sequence and structure information across species to predict chemical susceptibility by querying a known sensitive species with the known chemical protein target and providing lines of evidence for structural conservation in other species. Connectivity with the National Center for Biotechnology Information and combination of their databases and executables make up the backend of the SeqAPASS tool. Linkages to DrugBank, the veterinary substances database, therapeutic target database, the toxin and toxin-target database, AOP-Wiki, and CompTox Chemicals Dashboard provide information needed for querying the SeqAPASS tool regarding sensitive species and chemical-protein targets. Autocompletion of a Boolean string to query Google Scholar from the SeqAPASS interface informs more advanced Levels of the SeqAPASS evaluation focusing on critical amino acid comparisons, whereas a widget to filter data from the ECOTOX knowledgebase provides opportunities to bring computational predictions of chemical susceptibility together with empirical data more rapidly. Ensuring the most useful information is available and linked to the user interface provides the ability to rapidly and systematically explore scientific questions and synthesize results as opposed to waste time searching for valuable information. To further advance the SeqAPASS pipeline, efforts are underway to incorporate tools for generating protein structural models, evaluating structural model quality, aligning structures, and generating additional metrics to improve understanding of protein conservation across species. This abstract neither constitutes nor necessarily reflects USEPA policy.
URLs/Downloads:
DOI: SeqAPASS implements strategic connections of knowledge streams to inform species extrapolation for chemical safety
LALONE_SEQAPASS.PDF (PDF, NA pp, 2056.444 KB, about PDF)