ShinyTPs: Curate transformation products from text mining results

peer reviewedPlatform Presentation at SETAC Europe 2023, Dublin, 30 April - 4 May 2023 Presentation 3.12.T-02, EcoCen Room, 9:05 am Thursday 4 May

Open and FAIR transformation product data for improved suspect/non-target screening: REFTPs in the NORMAN-SLE, PubChem and patRoon

peer reviewedPresentation given at ICCE, Venice, 11 - 15 June 2023

Per- and Polyfluoroalkyl Substances (PFAS) in PubChem: 7 Million and Growing.

peer reviewedPer- and polyfluoroalkyl substances (PFAS) are of high concern, with calls to regulate them as a class. In 2021, the Organisation for Economic Co-operation and Development (OECD) revised the definition of PFAS to include any chemical containing at least one saturated CF2 or CF3 moiety. The consequence is that one of the largest open chemical collections, PubChem, with 116 million compounds, now contains over 7 million PFAS under this revised definition. These numbers are several orders of magnitude higher than previously established PFAS lists (typically thousands of entries) and pose an incredible challenge to researchers and computational workflows alike. This article describes a dynamic, openly accessible effort to navigate and explore the >7 million PFAS and >21 million fluorinated compounds (September 2023) in PubChem by establishing the "PFAS and Fluorinated Compounds in PubChem" Classification Browser (or "PubChem PFAS Tree"). A total of 36500 nodes support browsing of the content according to several categories, including classification, structural properties, regulatory status, or presence in existing PFAS suspect lists. Additional annotation and associated data can be used to create subsets (and thus manageable suspect lists or databases) of interest for a wide range of environmental, regulatory, exposomics, and other applications

ShinyTPs: Curating Transformation Products from Text Mining Results.

peer reviewedTransformation 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.U-AGR-8049 - H2020 - ZeroPM (01/10/2021 - 30/09/2026) - SCHYMANSKI Emm

Dioxin2023 Plenary: Exploring Millions of PFAS with FAIR and Open Science

editorial reviewedPlenary presentation for Dioxin 2023 in Maastricht - Tuesday 12 September Exploring Millions of PFAS with FAIR and Open Science This presentation features a sound track created by Jamie Perera (slide 27) on "Our Chemical Past, Present and Future", which can be downloaded on Vimeo (video) or Soundcloud (sound only). Please leave feedback there if you enjoy it

The NORMAN Suspect List Exchange (NORMAN-SLE): facilitating European and worldwide collaboration on suspect screening in high resolution mass spectrometry

Background: The NORMAN Association (https://www.norman-.network.com/) initiated the NORMAN Suspect List Exchange (NORMAN-SLE; https://www.norman-.network.com/nds/SLE/) in 2015, following the NORMAN collaborative trial on non-target screening of environmental water samples by mass spectrometry. Since then, this exchange of information on chemicals that are expected to occur in the environment, along with the accompanying expert knowledge and references, has become a valuable knowledge base for "suspect screening" lists. The NORMAN-SLE now serves as a FAIR (Findable, Accessible, Interoperable, Reusable) chemical information resource worldwide.Results: The NORMAN-SLE contains 99 separate suspect list collections (as of May 2022) from over 70 contributors around the world, totalling over 100,000 unique substances. The substance classes include per- and polyfluoroalkyl substances (PFAS), pharmaceuticals, pesticides, natural toxins, high production volume substances covered under the European REACH regulation (EC: 1272/2008), priority contaminants of emerging concern (CECs) and regulatory lists from NORMAN partners. Several lists focus on transformation products (TPs) and complex features detected in the environment with various levels of provenance and structural information. Each list is available for separate download. The merged, curated collection is also available as the NORMAN Substance Database (NORMAN SusDat). Both the NORMAN-SLE and NORMAN SusDat are integrated within the NORMAN Database System (NDS). The individual NORMAN-SLE lists receive digital object identifiers (DOIs) and traceable versioning via a Zenodo community (https:// zenodo.org/communities/norman-.sle), with a total of > 40,000 unique views, > 50,000 unique downloads and 40 citations (May 2022). NORMAN-SLE content is progressively integrated into large open chemical databases such as PubChem (https://pubchem.ncbi.nlm.nih.gov/) and the US EPA's CompTox Chemicals Dashboard (https://comptox. epa.gov/dashboard/), enabling further access to these lists, along with the additional functionality and calculated properties these resources offer. PubChem has also integrated significant annotation content from the NORMAN-SLE, including a classification browser (https://pubchem.ncbi.nlm.nih.gov/classification/#hid=101).Conclusions: The NORMAN-SLE offers a specialized service for hosting suspect screening lists of relevance for the environmental community in an open, FAIR manner that allows integration with other major chemical resources. These efforts foster the exchange of information between scientists and regulators, supporting the paradigm shift to the "one substance, one assessment" approach. New submissions are welcome via the contacts provided on the NORMAN-SLE website (https://www.norman-.network.com/nds/SLE/)

The NORMAN Suspect List Exchange (NORMAN-SLE): Facilitating European and worldwide collaboration on suspect screening in high resolution mass spectrometry

Background: The NORMAN Association (https://www.norman-network.com/) initiated the NORMAN Suspect List Exchange (NORMAN-SLE; https://www.norman-network.com/nds/SLE/) in 2015, following the NORMAN collaborative trial on non-target screening of environmental water samples by mass spectrometry. Since then, this exchange of information on chemicals that are expected to occur in the environment, along with the accompanying expert knowledge and references, has become a valuable knowledge base for “suspect screening” lists. The NORMAN-SLE now serves as a FAIR (Findable, Accessible, Interoperable, Reusable) chemical information resource worldwide. Results: The NORMAN-SLE contains 99 separate suspect list collections (as of May 2022) from over 70 contributors around the world, totalling over 100,000 unique substances. The substance classes include per- and polyfluoroalkyl substances (PFAS), pharmaceuticals, pesticides, natural toxins, high production volume substances covered under the European REACH regulation (EC: 1272/2008), priority contaminants of emerging concern (CECs) and regulatory lists from NORMAN partners. Several lists focus on transformation products (TPs) and complex features detected in the environment with various levels of provenance and structural information. Each list is available for separate download. The merged, curated collection is also available as the NORMAN Substance Database (NORMAN SusDat). Both the NORMAN-SLE and NORMAN SusDat are integrated within the NORMAN Database System (NDS). The individual NORMAN-SLE lists receive digital object identifiers (DOIs) and traceable versioning via a Zenodo community (https://zenodo.org/communities/norman-sle), with a total of > 40,000 unique views, > 50,000 unique downloads and 40 citations (May 2022). NORMAN-SLE content is progressively integrated into large open chemical databases such as PubChem (https://pubchem.ncbi.nlm.nih.gov/) and the US EPA’s CompTox Chemicals Dashboard (https://comptox.epa.gov/dashboard/), enabling further access to these lists, along with the additional functionality and calculated properties these resources offer. PubChem has also integrated significant annotation content from the NORMAN-SLE, including a classification browser (https://pubchem.ncbi.nlm.nih.gov/classification/#hid=101). Conclusions: The NORMAN-SLE offers a specialized service for hosting suspect screening lists of relevance for the environmental community in an open, FAIR manner that allows integration with other major chemical resources. These efforts foster the exchange of information between scientists and regulators, supporting the paradigm shift to the “one substance, one assessment” approach. New submissions are welcome via the contacts provided on the NORMAN-SLE website (https://www.norman-network.com/nds/SLE/)

The NORMAN Suspect List Exchange (NORMAN-SLE): facilitating European and worldwide collaboration on suspect screening in high resolution mass spectrometry

The NORMAN Association (https://www.norman-network.com/) initiated the NORMAN Suspect List Exchange (NORMAN-SLE; https://www.norman-network.com/nds/SLE/) in 2015, following the NORMAN collaborative trial on non-target screening of environmental water samples by mass spectrometry. Since then, this exchange of information on chemicals that are expected to occur in the environment, along with the accompanying expert knowledge and references, has become a valuable knowledge base for "suspect screening" lists. The NORMAN-SLE now serves as a FAIR (Findable, Accessible, Interoperable, Reusable) chemical information resource worldwide.The NORMAN-SLE project has received funding from the NORMAN Association via its joint proposal of activities. HMT and ELS are supported by the Luxembourg National Research Fund (FNR) for project A18/BM/12341006. ELS, PC, SEH, HPHA, ZW acknowledge funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 101036756, project ZeroPM: Zero pollution of persistent, mobile substances. The work of EEB, TC, QL, BAS, PAT, and JZ was supported by the National Center for Biotechnology Information of the National Library of Medicine (NLM), National Institutes of Health (NIH). JOB is the recipient of an NHMRC Emerging Leadership Fellowship (EL1 2009209). KVT and JOB acknowledge the support of the Australian Research Council (DP190102476). The Queensland Alliance for Environmental Health Sciences, The University of Queensland, gratefully acknowledges the financial support of the Queensland Department of Health. NR is supported by a Miguel Servet contract (CP19/00060) from the Instituto de Salud Carlos III, co-financed by the European Union through Fondo Europeo de Desarrollo Regional (FEDER). MM and TR gratefully acknowledge financial support by the German Ministry for Education and Research (BMBF, Bonn) through the project “Persistente mobile organische Chemikalien in der aquatischen Umwelt (PROTECT)” (FKz: 02WRS1495 A/B/E). LiB acknowledges funding through a Research Foundation Flanders (FWO) fellowship (11G1821N). JAP and JMcL acknowledge financial support from the NIH for CCSCompendium (S50 CCSCOMPEND) via grants NIH NIGMS R01GM092218 and NIH NCI 1R03CA222452-01, as well as the Vanderbilt Chemical Biology Interface training program (5T32GM065086-16), plus use of resources of the Center for Innovative Technology (CIT) at Vanderbilt University. TJ was (partly) supported by the Dutch Research Council (NWO), project number 15747. UFZ (TS, MaK, WB) received funding from SOLUTIONS project (European Union’s Seventh Framework Programme for research, technological development and demonstration under Grant Agreement No. 603437). TS, MaK, WB, JPA, RCHV, JJV, JeM and MHL acknowledge HBM4EU (European Union’s Horizon 2020 research and innovation programme under the grant agreement no. 733032). TS acknowledges funding from NFDI4Chem—Chemistry Consortium in the NFDI (supported by the DFG under project number 441958208). TS, MaK, WB and EMLJ acknowledge NaToxAq (European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie Grant Agreement No. 722493). S36 and S63 (HPHA, SEH, MN, IS) were funded by the German Federal Ministry for the Environment, Nature Conservation and Nuclear Safety (BMU) Project No. (FKZ) 3716 67 416 0, updates to S36 (HPHA, SEH, MN, IS) by the German Federal Ministry for the Environment, Nature Conservation, Nuclear Safety and Consumer Protection (BMUV) Project No. (FKZ) 3719 65 408 0. MiK acknowledges financial support from the EU Cohesion Funds within the project Monitoring and assessment of water body status (No. 310011A366 Phase III). The work related to S60 and S82 was funded by the Swiss Federal Office for the Environment (FOEN), KK and JH acknowledge the input of Kathrin Fenner’s group (Eawag) in compiling transformation products from European pesticides registration dossiers. DSW and YDF were supported by the Canadian Institutes of Health Research and Genome Canada. The work related to S49, S48 and S77 was funded by the MAVA foundation; for S77 also the Valery Foundation (KG, JaM, BG). DML acknowledges National Science Foundation Grant RUI-1306074. YL acknowledges the National Natural Science Foundation of China (Grant No. 22193051 and 21906177), and the Chinese Postdoctoral Science Foundation (Grant No. 2019M650863). WLC acknowledges research project 108C002871 supported by the Environmental Protection Administration, Executive Yuan, R.O.C. Taiwan (Taiwan EPA). JG acknowledges funding from the Swiss Federal Office for the Environment. AJW was funded by the U.S. Environmental Protection Agency. LuB, AC and FH acknowledge the financial support of the Generalitat Valenciana (Research Group of Excellence, Prometeo 2019/040). KN (S89) acknowledges the PhD fellowship through Marie Skłodowska-Curie grant agreement No. 859891 (MSCA-ETN). Exposome-Explorer (S34) was funded by the European Commission projects EXPOsOMICS FP7-KBBE-2012 [308610]; NutriTech FP7-KBBE-2011-5 [289511]; Joint Programming Initiative FOODBALL 2014–17. CP acknowledges grant RYC2020-028901-I funded by MCIN/AEI/1.0.13039/501100011033 and “ESF investing in your future”, and August T Larsson Guest Researcher Programme from the Swedish University of Agricultural Sciences. The work of ML, MaSe, SG, TL and WS creating and filling the STOFF-IDENT database (S2) mostly sponsored by the German Federal Ministry of Education and Research within the RiSKWa program (funding codes 02WRS1273 and 02WRS1354). XT acknowledges The National Food Institute, Technical University of Denmark. MaSch acknowledges funding by the RECETOX research infrastructure (the Czech Ministry of Education, Youth and Sports, LM2018121), the CETOCOEN PLUS project (CZ.02.1.01/0.0/0.0/15_003/0000469), and the CETOCOEN EXCELLENCE Teaming 2 project supported by the Czech ministry of Education, Youth and Sports (No CZ.02.1.01/0.0/0.0/17_043/0009632).Peer reviewe

S74 | REFTPS | Transformation Products and Reactions from Literature

<p>This is the collection associated with list S74 REFTPS Transformation Products and Reactions from Literature on the NORMAN Suspect List Exchange.</p><p><a href="https://www.norman-network.com/nds/SLE/">https://www.norman-network.com/nds/SLE/</a></p><p>This dataset is designed to provide an entry point for users to contribute transformation products and reactions documented in the literature for addition to the NORMAN SLE, SusDat and the PubChem Transformations section.</p><p>Change logs and version tracking at the <a href="https://git-r3lab.uni.lu/eci/pubchem/-/tree/master/annotations/tps/REFTPS">ECI GitLab site</a>.</p><p>Change log: v0.0.2 added InChIKey file. v0.1.0 added new reactions from Anca Baesu and DTXSIDs. v0.2.0 added PFAS TPs from Parviel Chirsir. v0.2.1 more PFAS TPs from Parviel. v0.3.0 Emma added HMMM TPs; v0.3.1 updated references and added new CIDs; added new MS/MS file. v0.4.0 new PFAS TPs plus MS/MS and NMR. v0.4.1 new CID added, plus CID 67543 updated to 14571268. v0.5.0 new 8:2 FT TPs plus annotation data; new structures. v0.5.1 added new CIDs. v0.5.2 added 2:2 to 6:2 FT TPs, updated ref for Bugsel. v0.5.3: added new CIDs. v0.6.0 added new structures. v0.7.0 added more new structures. v 0.7.1: updated CIDs in substances, fixed PFHpA mapping in transformations (some were mismapped to CID 67819). v 0.7.2: updated Biosystem description for many records. v0.8.0: updated CID 163201609 => 166001338, adjusted last 4 MS/MS, added Barisci AOP transformations. v0.9.0 added new structures. v0.9.1 updated CIDs and added radical structures from deposition. v0.10.0 added new irgarol reaction; v0.10.1 added new CID. v0.11.0 added Avendano and Mabury transformations from Parviel. v0.12.0 added Washington MS/MS and Marjanovic MS/MS and reactions. v0.13.0 added Galaxolide transformation. v0.14.0 added Zweigle PFAS TPs with MSMS. v0.14.1 added new CIDs. v0.15.0 added antibiotic TPs from Paul Löffler, SLU, incl. entries with no CID. </p>NOTE: This deposition is continually updating as new data is added

S74 | REFTPS | Transformation Products and Reactions from Literature

<p>This is the collection associated with list S74 REFTPS Transformation Products and Reactions from Literature on the NORMAN Suspect List Exchange.</p><p><a href="https://www.norman-network.com/nds/SLE/">https://www.norman-network.com/nds/SLE/</a></p><p>This dataset is designed to provide an entry point for users to contribute transformation products and reactions documented in the literature for addition to the NORMAN SLE, SusDat and the PubChem Transformations section.</p><p>Change logs and version tracking at the <a href="https://git-r3lab.uni.lu/eci/pubchem/-/tree/master/annotations/tps/REFTPS">ECI GitLab site</a>.</p><p>Change log: v0.0.2 added InChIKey file. v0.1.0 added new reactions from Anca Baesu and DTXSIDs. v0.2.0 added PFAS TPs from Parviel Chirsir. v0.2.1 more PFAS TPs from Parviel. v0.3.0 Emma added HMMM TPs; v0.3.1 updated references and added new CIDs; added new MS/MS file. v0.4.0 new PFAS TPs plus MS/MS and NMR. v0.4.1 new CID added, plus CID 67543 updated to 14571268. v0.5.0 new 8:2 FT TPs plus annotation data; new structures. v0.5.1 added new CIDs. v0.5.2 added 2:2 to 6:2 FT TPs, updated ref for Bugsel. v0.5.3: added new CIDs. v0.6.0 added new structures. v0.7.0 added more new structures. v 0.7.1: updated CIDs in substances, fixed PFHpA mapping in transformations (some were mismapped to CID 67819). v 0.7.2: updated Biosystem description for many records. v0.8.0: updated CID 163201609 => 166001338, adjusted last 4 MS/MS, added Barisci AOP transformations. v0.9.0 added new structures. v0.9.1 updated CIDs and added radical structures from deposition. v0.10.0 added new irgarol reaction; v0.10.1 added new CID. v0.11.0 added Avendano and Mabury transformations from Parviel. v0.12.0 added Washington MS/MS and Marjanovic MS/MS and reactions. v0.13.0 added Galaxolide transformation. v0.14.0 added Zweigle PFAS TPs with MSMS. v0.14.1 added new CIDs. v0.15.0 added antibiotic TPs from Paul Löffler, SLU, incl. entries with no CID. v0.15.1 added new CIDs.</p>NOTE: This deposition is continually updating as new data is added