[OA Week] Making Chemical Data Available - Telling stories about chemicals

Slides available at DOI: 10.5281/zenodo.17469430 Prof. Dr. Emma L. Schymanski (plus many, many colleagues and collaborators!) Environmental Cheminformatics Group, Luxembourg Centre for Systems Biomedicine, University of Luxembourg [email protected] / https://gitlab.com/uniluxembourg/lcsb/eci https://wwwen.uni.lu/lcsb/research/environmental_cheminformatics/ Uni.lu – Open Access Week Training – 29 Oct. 2025 https://www.uni.lu/llc-en/open-access-week-2025-2/ Making Chemical Data Available Telling stories about chemicals Overview •Welcome to Open Access Week at UL! oWhat is Open? What is FAIR? oIntroduction & Motivation for Research •From Bellevue to Belval – My Chemical Data Story oDeveloping Open Cheminformatic Resources oCommunicating (Scary) Science to the Public •Take home messages 2 3 Open Science Working Group at the University of Luxembourg https://www.uni.lu/en/about/organisation/administration/#special-advisors 4 environment environmental sample high resolution mass spectrometry cheminformatics identify chemicals and toxic effects Our Research (Environmental Cheminformatics) & Open Science https://www.uni.lu/lcsb-en/research-groups/environmental-cheminformatics/ 5 environment environmental sample high resolution mass spectrometry cheminformatics identify chemicals and toxic effects Our Research (Environmental Cheminformatics) & Open Science Definitions of Data Sharing: Open and FAIR Science •Open access & open source are a subset of Open Science: –Research outputs are distributed online, free of cost or access barriers –Open source typically refers to code, open access to data –Open access => CC-0, CC-BY etc; Open source => GPL, Apache etc. •The FAIR principles – how to make data: –Findable, –Accessible, –Interoperable and –Reusable P Suber: http://legacy.earlham.edu/~peters/fos/overview.htm & GO FAIR: https://www.go-fair.org/fair-principles/ & MD Wilkinson et al. DOI:10.1038/sdata.2016.18 & EL Schymanski and EE Bolton DOI: 10.1093/exposome/osab006 https://commons.wikimedia.org/wiki/File:FAIR_data_principles.jpg “as open as possible, as closed as necessary” 6 FAIR and Open Science https://commons.wikimedia.org/wiki/File:FAIR_data_principles.jpg Schymanski & Schymanski (2023) Nature Water. DOI: 10.1038/s44221-022-00014-z 7 Motivation: Delving into the Chemical Unknown 8 https://knowledge.aidr.org.au/resources/industrial-bellevue-hazardous-waste-fire/ Motivation: Delving into the Chemical Unknown 9 https://www.cas.org/cas-data/cas-registry CLOSED ACCESS Mass Spectral Libraries: MassBank (Open Source & Data!) https://massbank.eu/MassBank/ https://github.com/MassBank/MassBank-data/ 16 Elapavalore et al. (2023) DOI: 10.1039/D3EM00181D Neumann et al. (accepted) Nucleic Acid Research Database Issue MassBank.EU – Environmental Data Contributions 17 https://massbank.eu/MassBank/content Mass Spectral Libraries: MassBank (Open Source & Data!) https://massbank.eu/MassBank/ https://github.com/MassBank/MassBank-data/ 18 Elapavalore et al. (2023) DOI: 10.1039/D3EM00181D Gathering Expert Knowledge: NORMAN-SLE https://www.norman-network.com/nds/SLE/ 19 Mohammed Taha et al. (2022) DOI: 10.1186/s12302-022-00680-6 Gathering Expert Knowledge: NORMAN-SLE https://www.norman-network.com/nds/SLE/ 20 Mohammed Taha et al. (2022) DOI: 10.1186/s12302-022-00680-6 Gathering Expert Knowledge: NORMAN-SLE https://www.norman-network.com/nds/SLE/ 21 Mohammed Taha et al. (2022) DOI: 10.1186/s12302-022-00680-6 Suspect List(s) (NORMAN-SLE) (NORMAN SusDat) NORMAN Database System (NDS) Mohammed Taha et al. (2022) DOI: 10.1186/s12 302-02200680-6 22 Suspect List(s) (NORMAN-SLE) (NORMAN SusDat) NORMAN Database System (NDS) Mohammed Taha et al. (2022) DOI: 10.1186/s12 302-02200680-6 23 Alygizakis et al, 2019, TrAC, DOI: 10.1016/j.trac.2019.04.008 Suspect List(s) (NORMAN-SLE) (NORMAN SusDat) NORMAN Database System (NDS) Mohammed Taha et al. (2022) DOI: 10.1186/s12 302-02200680-6 24 Alygizakis et al, 2019, TrAC, DOI: 10.1016/j.trac.2019.04.008 Suspect List(s) (NORMAN-SLE) (NORMAN SusDat) NORMAN Database System (NDS) Mohammed Taha et al. (2022) DOI: 10.1186/s12 302-02200680-6 25 for Exposomics 32 http://pubchemlite.lcsb.uni.lu/ caffeine Database: for Exposomics 33 https://pubchemlite.lcsb.uni.lu/e/compound/2519 caffeine Database: for Exposomics 34 https://pubchemlite.lcsb.uni.lu/e/compound/2519 Database: for Exposomics 35 https://pubchemlite.lcsb.uni.lu/e/compound/2519 Aurich et al. (2024) ES&T Letters DOI: 10.1021/acs.estlett. 4c00560 caffeine The Chemical Stripes and Patent Data Left: Neuwald et al, STOTEN, DOI: 10.1016/j.scitotenv.2023.163921 Photo of Daniel Zahn, UFZ at SETAC Europe, 30 April – 4 May, 2023. Image reused with permission EV 36 (live stripe calculations during SETAC 2023) …and now in 2025: Fluorinated ions are everywhere… Tisler et al. (2025) DOI: 10.1021/acs.est.5c06876 37 Elapavalore et al. (2025) DOI: 10.1021/acs.estlett.4c01003 & Schymanski et al. (2021) DOI: 10.1186/s13321-021-00489-0 38 : Fewer and more relevant candidates – with context Putting to work: NTS in Luxembourg 39 271 surface water samples (2019-2022) Target Monitoring Complementary NTS “No river in good condition” (2022) Slide: D. Aurich, PhD Defense. Ref: Aurich et al (2023)Env. Sci. Europe. DOI: 10.1186/s12302-023-00805-5 Putting to work: NTS in Luxembourg 40 Slide: D. Aurich, PhD Defense. Ref: Aurich et al (2023)Env. Sci. Europe. DOI: 10.1186/s12302-023-00805-5 COVID Pesticide spraying Temporal variations Classification Known Use Disorder/ Disease Pharmaceuticals Agrochem ~99 % ~75 % ~60 % ~15 % Putting to work: NTS in Luxembourg •41 frequentlyoccurring chemicals not (yet) monitored Slide mod. from: D. Aurich, PhD Defense. Ref: Aurich et al (2023)Env. Sci. Europe. DOI: 10.1186/s12302-023-00805-5 Synonym Use Parent Name PubChem CID No of occurrences Irbesartan pharmaceutical -3749 32 Amisulpride pharmaceutical -2159 31 Telmisartan pharmaceutical -65999 26 Celiprolol pharmaceutical -2663 25 Fluconazole pharmaceutical -3365 25 Trimethoprim pharmaceutical -5578 24 4-Acetamidoantipyrine pharmaceutical Metamizole 65743 23 4-NP industrial -980 22 Desvenlafaxine pharmaceutical Venlafaxine 125017 22 TCEP flame retardant -8295 19 TCPP flame retardant -26176 19 Triethyl phosphate industrial -6535 18 Adipic acid industrial -196 18 4-Formylaminoantipyrine pharmaceutical Aminopyrine 72666 17 Carbamazepine-10,11-epoxide pharmaceutical Carbamazepine 2555 15 Dibutyl phthalate industrial -3026 14 PFOA industrial -9554 14 2-Hydroxycarbamazepine pharmaceutical Carbamazepine 129274 14 3-Hydroxypyridine industrial -7971 13 Tributylamine industrial -7622 13 D617 pharmaceutical Verapamil 93168 13 Sulisobenzone consumer products -19988 13 Ensulizole consumer products -33919 13 Pharmaceuticals Industrial chemicals 41 Browsing Dead-End (and other) Predicted TPs 48 https://gcitps.lcsb.uni.lu/ & Palm et al. (2025) Presentation at SETAC Europe, 13 May 2025. DOI: 10.5281/zenodo.15574837 Predicting Dead-end Transformation Products 49 Source: Emma Palm. Palm et al. (2025) Presentation at SETAC Europe, 13 May 2025. DOI: 10.5281/zenodo.15574837. Number of precursors: 170 Overview •Welcome to Open Access Week at UL! oWhat is Open? What is FAIR? oIntroduction & Motivation for Research •From Bellevue to Belval – My Chemical Data Story oDeveloping Open Cheminformatic Resources oCommunicating (Scary) Science to the Public •Take home messages 50 World Water Day – Forever Chemicals https://www.uni.lu/lcsb-en/news/forever-chemicals-diving-into-troubled-waters/ The source of open PFAS data? 52 Glüge et al. (2020) ESPI, DOI: 10.1039/d0em00291g Bugsel et al. (2022) ABC, 414, 1217-1225. DOI:10.1007/s00216-021-03463-9 https://pubchem.ncbi.nlm.nih.gov/compound/156620404#section=1H-NMR-Spectra https://twitter.com/AcademicTox/ status/1605997310726443009 Parviel Chirsir @PChirsir …and many more! https://tarheels.live/bakerlab/ Éiwegkeetschemikalie / polluants éternels / Forever chemicals? 53 https://today.rtl.lu/news/luxembourg/a/2242399.html / https://www.rtl.lu/news/national/a/2242278.html / https://infos.rtl.lu/actu/luxem bourg/a/2242403.html https://www.100komma7.lu/news/Invitee-vum-Dag-Emma-Schymanski?pd=radio FAIR-TPs – How much do we really know about TFA? 54 Mayahi, Palm & Schymanski (in prep.). https://fairtps.lcsb.uni.lu/ 18 known data points in FAIR-TPs Schymanski et al. (2023) ES&T DOI: 10.1021/acs.est.3c04855 3D Stories => 3D Molecules 55 https://3dmolecules.netlify.app/ 56 28-Oct-25 Environmental Cheminformatics @ LCSB, Uni.lu FAIR chemical data Open source mass spectral library HRMS NTS TP workflows Slide inspired by B. Talavera Explore chemical space Browse transformations 57 Storytelling