Transformation products; Text mining; Non-target analysis; FAIR
Abstract :
[en] Transformation product (TP) information is essential to accurately evaluate the hazards compounds pose to human health and the environment. However, information about TPs is often limited, and existing data is often not fully Findable, Accessible, Interoperable, and Reusable (FAIR). FAIRifying existing TP knowledge is a relatively easy path toward improving access to data for identification workflows and for machine-learning-based algorithms. ShinyTPs was developed to curate existing transformation information derived from text-mined data within the PubChem database. The application (available as an R package) visualizes the text-mined chemical names to facilitate the user validation of the automatically extracted reactions. ShinyTPs was applied to a case study using 436 tentatively identified compounds to prioritize TP retrieval. This resulted in the extraction of 645 reactions (associated with 496 compounds), of which 319 were not previously available in PubChem. The curated reactions were added to the PubChem Transformations library, which was used as a TP suspect list for identification of TPs using the open-source workflow patRoon. In total, 72 compounds from the library were tentatively identified, 18% of which were curated using ShinyTPs, showing that the app can help support TP identification in non-target analysis workflows.
Research center :
Luxembourg Centre for Systems Biomedicine (LCSB): Environmental Cheminformatics (Schymanski Group)
Disciplines :
Chemistry
Author, co-author :
PALM, Emma Helena ; University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > Environmental Cheminformatics
CHIRSIR, Parviel ; University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > Environmental Cheminformatics
KRIER, Jessy ; University of Luxembourg > Luxembourg Centre for Systems Biomedicine > Environmental Cheminformatics > Team Emma SCHYMANSKI
Thiessen, Paul A ; National Center for Biotechnology Information (NCBI), National Library of Medicine (NLM), National Institutes of Health (NIH), Bethesda, Maryland 20894, United States
Zhang, Jian; National Center for Biotechnology Information (NCBI), National Library of Medicine (NLM), National Institutes of Health (NIH), Bethesda, Maryland 20894, United States
Bolton, Evan E ; National Center for Biotechnology Information (NCBI), National Library of Medicine (NLM), National Institutes of Health (NIH), Bethesda, Maryland 20894, United States
H2020 Environment Fonds National de la Recherche Luxembourg U.S. National Library of Medicine Union Européenne
Funding number :
01036756
Funding text :
The work of P.A.T., J.Z., and E.E.B. was supported by the National Center for Biotechnology Information of the National Library of Medicine (NLM), National Institutes of Health. E.L.S. acknowledges funding support from the Luxembourg National Research Fund (FNR) for project A18/BM/12341006. E.H.P., E.L.S., and P.C. acknowledge funding from the European Union’s Horizon 2020 research and innovation program under Grant Agreement No. 101036756 for project “ZeroPM: Zero pollution of persistent, mobile substances”.
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