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7. Database resources of the National Center for Biotechnology Information in 2025.

Author

Sayers, Eric W, Beck, Jeffrey, Bolton, Evan E, Brister, J Rodney, Chan, Jessica, Connor, Ryan, Feldgarden, Michael, Fine, Anna M, Funk, Kathryn, Hoffman, Jinna, Kannan, Sivakumar, Kelly, Christopher, Klimke, William, Kim, Sunghwan, Lathrop, Stacy, Marchler-Bauer, Aron, Murphy, Terence D, O'Sullivan, Chris, Schmieder, Erin, and Skripchenko, Yuriy

Published
2025
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8. PubChem 2025 update.

Author

Kim, Sunghwan, Chen, Jie, Cheng, Tiejun, Gindulyte, Asta, He, Jia, He, Siqian, Li, Qingliang, Shoemaker, Benjamin A, Thiessen, Paul A, Yu, Bo, Zaslavsky, Leonid, Zhang, Jian, and Bolton, Evan E

Published
2025
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10. The NORMAN Suspect List Exchange (NORMAN-SLE): facilitating European and worldwide collaboration on suspect screening in high resolution mass spectrometry

Author

Mohammed Taha, Hiba, Aalizadeh, Reza, Alygizakis, Nikiforos, Antignac, Jean-Philippe, Arp, Hans Peter H., Bade, Richard, Baker, Nancy, Belova, Lidia, Bijlsma, Lubertus, Bolton, Evan E., Brack, Werner, Celma, Alberto, Chen, Wen-Ling, Cheng, Tiejun, Chirsir, Parviel, Čirka, Ľuboš, D’Agostino, Lisa A., Djoumbou Feunang, Yannick, Dulio, Valeria, Fischer, Stellan, Gago-Ferrero, Pablo, Galani, Aikaterini, Geueke, Birgit, Głowacka, Natalia, Glüge, Juliane, Groh, Ksenia, Grosse, Sylvia, Haglund, Peter, Hakkinen, Pertti J., Hale, Sarah E., Hernandez, Felix, Janssen, Elisabeth M.-L., Jonkers, Tim, Kiefer, Karin, Kirchner, Michal, Koschorreck, Jan, Krauss, Martin, Krier, Jessy, Lamoree, Marja H., Letzel, Marion, Letzel, Thomas, Li, Qingliang, Little, James, Liu, Yanna, Lunderberg, David M., Martin, Jonathan W., McEachran, Andrew D., McLean, John A., Meier, Christiane, Meijer, Jeroen, Menger, Frank, Merino, Carla, Muncke, Jane, Muschket, Matthias, Neumann, Michael, Neveu, Vanessa, Ng, Kelsey, Oberacher, Herbert, O’Brien, Jake, Oswald, Peter, Oswaldova, Martina, Picache, Jaqueline A., Postigo, Cristina, Ramirez, Noelia, Reemtsma, Thorsten, Renaud, Justin, Rostkowski, Pawel, Rüdel, Heinz, Salek, Reza M., Samanipour, Saer, Scheringer, Martin, Schliebner, Ivo, Schulz, Wolfgang, Schulze, Tobias, Sengl, Manfred, Shoemaker, Benjamin A., Sims, Kerry, Singer, Heinz, Singh, Randolph R., Sumarah, Mark, Thiessen, Paul A., Thomas, Kevin V., Torres, Sonia, Trier, Xenia, van Wezel, Annemarie P., Vermeulen, Roel C. H., Vlaanderen, Jelle J., von der Ohe, Peter C., Wang, Zhanyun, Williams, Antony J., Willighagen, Egon L., Wishart, David S., Zhang, Jian, Thomaidis, Nikolaos S., Hollender, Juliane, Slobodnik, Jaroslav, and Schymanski, Emma L.

Published
2022
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12. PubChem Periodic Table and Element pages: improving access to information on chemical elements from authoritative sources

Author

Kim Sunghwan, Gindulyte Asta, Zhang Jian, Thiessen Paul A., and Bolton Evan E.

Subjects
chemical database, chemical element, periodic table, pubchem, Chemistry, QD1-999
Abstract

PubChem (https://pubchem.ncbi.nlm.nih.gov) is one of the top five most visited chemistry web sites in the world, with more than five million unique users per month (as of March 2020). Many of these users are educators, undergraduate students, and graduate students at academic institutions. Therefore, PubChem has a great potential as an online resource for chemical education. This paper describes the PubChem Periodic Table and Element pages, which were recently introduced to celebrate the 150th anniversary of the periodic table. These services help users navigate the abundant chemical element data available within PubChem, while providing a convenient entry point to explore additional chemical content, such as biological activities and health and safety data available in PubChem Compound pages for specific elements and their isotopes. The PubChem Periodic Table and Element pages are also available as widgets, which enable web developers to display PubChem’s element data on web pages they design. The elemental data can be downloaded in common file formats and imported into data analysis programs (e.g., spreadsheet software, like Microsoft Excel and Google Sheets, and computer scripts, such as python and R). Overall, the PubChem Periodic Table and Element pages improve access to chemical element data from authoritative sources.

Published
2020
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15. Database resources of the National Center for Biotechnology Information

Author

Sayers, Eric W, primary, Beck, Jeff, additional, Bolton, Evan E, additional, Brister, J Rodney, additional, Chan, Jessica, additional, Comeau, Donald C, additional, Connor, Ryan, additional, DiCuccio, Michael, additional, Farrell, Catherine M, additional, Feldgarden, Michael, additional, Fine, Anna M, additional, Funk, Kathryn, additional, Hatcher, Eneida, additional, Hoeppner, Marilu, additional, Kane, Megan, additional, Kannan, Sivakumar, additional, Katz, Kenneth S, additional, Kelly, Christopher, additional, Klimke, William, additional, Kim, Sunghwan, additional, Kimchi, Avi, additional, Landrum, Melissa, additional, Lathrop, Stacy, additional, Lu, Zhiyong, additional, Malheiro, Adriana, additional, Marchler-Bauer, Aron, additional, Murphy, Terence D, additional, Phan, Lon, additional, Prasad, Arjun B, additional, Pujar, Shashikant, additional, Sawyer, Amanda, additional, Schmieder, Erin, additional, Schneider, Valerie A, additional, Schoch, Conrad L, additional, Sharma, Shobha, additional, Thibaud-Nissen, Françoise, additional, Trawick, Barton W, additional, Venkatapathi, Thilakam, additional, Wang, Jiyao, additional, Pruitt, Kim D, additional, and Sherry, Stephen T, additional

Published
2023
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17. ELIXIR and Toxicology: a community in development

Author

Martens, Marvin, primary, Stierum, Rob, additional, Schymanski, Emma L., additional, Evelo, Chris T., additional, Aalizadeh, Reza, additional, Aladjov, Hristo, additional, Arturi, Kasia, additional, Audouze, Karine, additional, Babica, Pavel, additional, Berka, Karel, additional, Bessems, Jos, additional, Blaha, Ludek, additional, Bolton, Evan E., additional, Cases, Montserrat, additional, Damalas, Dimitrios Ε., additional, Dave, Kirtan, additional, Dilger, Marco, additional, Exner, Thomas, additional, Geerke, Daan P., additional, Grafström, Roland, additional, Gray, Alasdair, additional, Hancock, John M., additional, Hollert, Henner, additional, Jeliazkova, Nina, additional, Jennen, Danyel, additional, Jourdan, Fabien, additional, Kahlem, Pascal, additional, Klanova, Jana, additional, Kleinjans, Jos, additional, Kondic, Todor, additional, Kone, Boï, additional, Lynch, Iseult, additional, Maran, Uko, additional, Martinez Cuesta, Sergio, additional, Ménager, Hervé, additional, Neumann, Steffen, additional, Nymark, Penny, additional, Oberacher, Herbert, additional, Ramirez, Noelia, additional, Remy, Sylvie, additional, Rocca-Serra, Philippe, additional, Salek, Reza M., additional, Sallach, Brett, additional, Sansone, Susanna-Assunta, additional, Sanz, Ferran, additional, Sarimveis, Haralambos, additional, Sarntivijai, Sirarat, additional, Schulze, Tobias, additional, Slobodnik, Jaroslav, additional, Spjuth, Ola, additional, Tedds, Jonathan, additional, Thomaidis, Nikolaos, additional, Weber, Ralf J.M., additional, van Westen, Gerard J.P., additional, Wheelock, Craig E., additional, Williams, Antony J., additional, Witters, Hilda, additional, Zdrazil, Barbara, additional, Županič, Anže, additional, and Willighagen, Egon L., additional

Published
2023
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20. Non-target LC-HRMS to Study the Exposome of Mild Cognitive Impairment and Alzheimer's Disease on Cerebrospinal Fluid

Author

Andújar, Begoña Talvavera, Mary, Arnaud, Cheng, Tiejun, Zaslavsky, Leonid, Bolton, Evan E., Heneka, Michael T., and Schymanski, Emma L.

Subjects
liquid chromatography, cheminformatics, CSF, Alzheimer's disease, High resolution mass spectrometry, exposomics
Abstract

This is the poster presentation number1142 for the19th Annual International Conference of theMetabolomicsSociety.

Published
2023
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21. Can Small Molecules Provide Clues on Disease Progression in Cerebrospinal Fluid from Mild Cognitive Impairment and Alzheimer’s Disease Patients?

Author

Talavera Andújar, Begoña, Mary, Arnaud, Venegas, Carmen, Cheng, Tiejun, Zaslavsky, Leonid, Bolton, Evan E., Heneka, Michael T., and Schymanski, Emma L.

Abstract

Alzheimer’s disease (AD) is a complex and multifactorial neurodegenerative disease, which is currently diagnosed via clinical symptoms and nonspecific biomarkers (such as Aβ1–42, t-Tau, and p-Tau) measured in cerebrospinal fluid (CSF), which alone do not provide sufficient insights into disease progression. In this pilot study, these biomarkers were complemented with small-molecule analysis using non-target high-resolution mass spectrometry coupled with liquid chromatography (LC) on the CSF of three groups: AD, mild cognitive impairment (MCI) due to AD, and a non-demented (ND) control group. An open-source cheminformatics pipeline based on MS-DIAL and patRoon was enhanced using CSF- and AD-specific suspect lists to assist in data interpretation. Chemical Similarity Enrichment Analysis revealed a significant increase of hydroxybutyrates in AD, including 3-hydroxybutanoic acid, which was found at higher levels in AD compared to MCI and ND. Furthermore, a highly sensitive target LC–MS method was used to quantify 35 bile acids (BAs) in the CSF, revealing several statistically significant differences including higher dehydrolithocholic acid levels and decreased conjugated BA levels in AD. This work provides several promising small-molecule hypotheses that could be used to help track the progression of AD in CSF samples.

Published
2024
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23. Adding open spectral data to MassBank and PubChem using open source tools to support non-targeted exposomics of mixtures

Author

Elapavalore, Anjana, Kondić, Todor, Singh, Randolph, Shoemaker, Benjamin A., Thiessen, Paul A., Zhang, Jian, Bolton, Evan E., Schymanski, Emma L., Elapavalore, Anjana, Kondić, Todor, Singh, Randolph, Shoemaker, Benjamin A., Thiessen, Paul A., Zhang, Jian, Bolton, Evan E., and Schymanski, Emma L.

Abstract

The term “exposome” is defined as a comprehensive study of life-course environmental exposures and the associated biological responses. Humans are exposed to many different chemicals, which can pose a major threat to the well-being of humanity. Targeted or non-targeted mass spectrometry techniques are widely used to identify and characterize various environmental stressors when linking exposures to human health. However, identification remains challenging due to the huge chemical space applicable to exposomics, combined with the lack of sufficient relevant entries in spectral libraries. Addressing these challenges requires cheminformatics tools and database resources to share curated open spectral data on chemicals to improve the identification of chemicals in exposomics studies. This article describes efforts to contribute spectra relevant for exposomics to the open mass spectral library MassBank (https://www.massbank.eu) using various open source software efforts, including the R packages RMassBank and Shinyscreen. The experimental spectra were obtained from ten mixtures containing toxicologically relevant chemicals from the US Environmental Protection Agency (EPA) Non-Targeted Analysis Collaborative Trial (ENTACT). Following processing and curation, 5582 spectra from 783 of the 1268 ENTACT compounds were added to MassBank, and through this to other open spectral libraries (e.g., MoNA, GNPS) for community benefit. Additionally, an automated deposition and annotation workflow was developed with PubChem to enable the display of all MassBank mass spectra in PubChem, which is rerun with each MassBank release. The new spectral records have already been used in several studies to increase the confidence in identification in non-target small molecule identification workflows applied to environmental and exposomics research.

Published
2023
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24. Database resources of the National Center for Biotechnology Information.

Author

Sayers, Eric W, Beck, Jeff, Bolton, Evan E, Brister, J Rodney, Chan, Jessica, Comeau, Donald C, Connor, Ryan, DiCuccio, Michael, Farrell, Catherine M, Feldgarden, Michael, Fine, Anna M, Funk, Kathryn, Hatcher, Eneida, Hoeppner, Marilu, Kane, Megan, Kannan, Sivakumar, Katz, Kenneth S, Kelly, Christopher, Klimke, William, and Kim, Sunghwan

Published
2024
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32. Database resources of the National Center for Biotechnology Information in 2023

Author

Sayers, Eric W, primary, Bolton, Evan E, additional, Brister, J Rodney, additional, Canese, Kathi, additional, Chan, Jessica, additional, Comeau, Donald C, additional, Farrell, Catherine M, additional, Feldgarden, Michael, additional, Fine, Anna M, additional, Funk, Kathryn, additional, Hatcher, Eneida, additional, Kannan, Sivakumar, additional, Kelly, Christopher, additional, Kim, Sunghwan, additional, Klimke, William, additional, Landrum, Melissa J, additional, Lathrop, Stacy, additional, Lu, Zhiyong, additional, Madden, Thomas L, additional, Malheiro, Adriana, additional, Marchler-Bauer, Aron, additional, Murphy, Terence D, additional, Phan, Lon, additional, Pujar, Shashikant, additional, Rangwala, Sanjida H, additional, Schneider, Valerie A, additional, Tse, Tony, additional, Wang, Jiyao, additional, Ye, Jian, additional, Trawick, Barton W, additional, Pruitt, Kim D, additional, and Sherry, Stephen T, additional

Published
2022
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33. PubChem 2023 update

Author

Kim, Sunghwan, primary, Chen, Jie, additional, Cheng, Tiejun, additional, Gindulyte, Asta, additional, He, Jia, additional, He, Siqian, additional, Li, Qingliang, additional, Shoemaker, Benjamin A, additional, Thiessen, Paul A, additional, Yu, Bo, additional, Zaslavsky, Leonid, additional, Zhang, Jian, additional, and Bolton, Evan E, additional

Published
2022
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36. The NORMAN Suspect List Exchange (NORMAN-SLE): Facilitating European and Worldwide Collaboration on Suspect Screening in High Resolution Mass Spectrometry

Author

Taha, Hiba Mohammed, primary, Aalizadeh, Reza, additional, Alygizakis, Nikiforos, additional, Antignac, Jean-Philippe, additional, Arp, Hans Peter H., additional, Bade, Richard, additional, Baker, Nancy, additional, Belova, Lidia, additional, Bijlsma, Lubertus, additional, Bolton, Evan E., additional, Brack, Werner, additional, Celma, Alberto, additional, Chen, Wen-Ling, additional, Cheng, Tiejun, additional, Chirsir, Parviel, additional, Čirka, Ľuboš, additional, D’Agostino, Lisa, additional, Feunang, Yannick Djoumbou, additional, Dulio, Valeria, additional, Fischer, Stellan, additional, Gago-Ferrero, Pablo, additional, Galani, Aikaterini, additional, Geueke, Birgit, additional, Głowacka, Natalia, additional, Glüge, Juliane, additional, Groh, Ksenia, additional, Grosse, Sylvia, additional, Haglund, Peter, additional, Hakkinen, Pertti J., additional, Hale, Sarah E., additional, Hernández, Félix, additional, Janssen, Elisabeth M.-L., additional, Jonkers, Tim, additional, Kiefer, Karin, additional, Kirchner, Michal, additional, Koschorreck, Jan, additional, Krauss, Martin, additional, Krier, Jessy, additional, Lamoree, Marja H., additional, Letzel, Marion, additional, Letzel, Thomas, additional, Li, Qingliang, additional, Little, James, additional, Liu, Yanna, additional, Lunderberg, David M., additional, Martin, Jonathan W., additional, McEachran, Andrew D., additional, McLean, John A., additional, Meier, Christiane, additional, Meijer, Jeroen, additional, Menger, Frank, additional, Merino, Carla, additional, Muncke, Jane, additional, Muschket, Matthias, additional, Neumann, Michael, additional, Neveu, Vanessa, additional, Ng, Kelsey, additional, Oberacher, Herbert, additional, O'Brien, Jake, additional, Oswald, Peter, additional, Oswaldova, Martina, additional, Picache, Jaqueline A., additional, Postigo, Cristina, additional, Ramírez, Noelia, additional, Reemtsma, Thorsten, additional, Renaud, Justin, additional, Rostkowski, Pawel, additional, Rüdel, Heinz, additional, Salek, Reza, additional, Samanipour, Saer, additional, Scheringer, Martin, additional, Schliebner, Ivo, additional, Schulz, Wolfgang, additional, Schulze, Tobias, additional, Sengl, Manfred, additional, Shoemaker, Benjamin A., additional, Sims, Kerry, additional, Singer, Heinz, additional, Singh, Randolph R., additional, Sumarah, Mark, additional, Thiessen, Paul A., additional, Thomas, Kevin V., additional, Torres, Sonia, additional, Trier, Xenia, additional, Wezel, Annemarie P. van, additional, Vermeulen, Roel C. H., additional, Vlaanderen, Jelle J., additional, Ohe, Peter C. von der, additional, Wang, Zhanyun, additional, Williams, Antony J., additional, Willighagen, Egon L., additional, Wishart, David S., additional, Zhang, Jian, additional, Thomaidis, Nikolaos S., additional, Hollender, Juliane, additional, Slobodnik, Jaroslav, additional, and Schymanski, Emma L., additional

Published
2022
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37. PubChem in 2021: new data content and improved web interfaces

Author

Kim, Sunghwan, Chen, Jie, Cheng, Tiejun, Gindulyte, Asta, He, Jia, He, Siqian, Li, Qingliang, Shoemaker, Benjamin A, Thiessen, Paul A, Yu, Bo, Zaslavsky, Leonid, Zhang, Jian, and Bolton, Evan E

Subjects
Coronavirus disease 2019 (COVID-19), AcademicSubjects/SCI00010, Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), Information Storage and Retrieval, Biology, World Wide Web, 03 medical and health sciences, User-Computer Interface, 0302 clinical medicine, Information resource, Drug Discovery, Genetics, Database Issue, Humans, Data content, Epidemics, 030304 developmental biology, 0303 health sciences, Internet, Data collection, business.industry, SARS-CoV-2, COVID-19, Data model, 030220 oncology & carcinogenesis, The Internet, Public Health, business, PubChem, Databases, Chemical, Software
Abstract

PubChem (https://pubchem.ncbi.nlm.nih.gov) is a popular chemical information resource that serves the scientific community as well as the general public, with millions of unique users per month. In the past two years, PubChem made substantial improvements. Data from more than 100 new data sources were added to PubChem, including chemical-literature links from Thieme Chemistry, chemical and physical property links from SpringerMaterials, and patent links from the World Intellectual Properties Organization (WIPO). PubChem's homepage and individual record pages were updated to help users find desired information faster. This update involved a data model change for the data objects used by these pages as well as by programmatic users. Several new services were introduced, including the PubChem Periodic Table and Element pages, Pathway pages, and Knowledge panels. Additionally, in response to the coronavirus disease 2019 (COVID-19) outbreak, PubChem created a special data collection that contains PubChem data related to COVID-19 and the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).

Published
2020

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

Author

Taha, Hiba Mohammed, Aalizadeh, Reza, Alygizakis, Nikiforos, Antignac, Jean-Philippe, Arp, Hans Peter H., Bade, Richard, Baker, Nancy, Belova, Lidia, Bijlsma, Lubertus, Bolton, Evan E., Brack, Werner, Celma, Alberto, Chen, Wen-Ling, Cheng, Tiejun, Chirsir, Parviel, Čirka, Ľuboš, D'Agostino, Lisa A., Feunang, Yannick Djoumbou, Dulio, Valeria, Fischer, Stellan, Gago-Ferrero, Pablo, Galani, Aikaterini, Geueke, Birgit, Głowacka, Natalia, Glüge, Juliane, Groh, Ksenia, Grosse, Sylvia, Haglund, Peter, Hakkinen, Pertti J., Hale, Sarah E., Hernandez, Felix, Janssen, Elisabeth M.-L., Jonkers, Tim, Kiefer, Karin, Kirchner, Michal, Koschorreck, Jan, Krauss, Martin, Krier, Jessy, Lamoree, Marja H., Letzel, Marion, Letzel, Thomas, Li, Qingliang, Little, James, Liu, Yanna, Lunderberg, David M., Martin, Jonathan W., McEachran, Andrew D., McLean, John A., Meier, Christiane, Meijer, Jeroen, Menger, Frank, Merino, Carla, Muncke, Jane, Muschket, Matthias, Neumann, Michael, Neveu, Vanessa, Ng, Kelsey, Oberacher, Herbert, O'Brien, Jake, Oswald, Peter, Oswaldova, Martina, Picache, Jaqueline A., Postigo, Cristina, Ramirez, Noelia, Reemtsma, Thorsten, Renaud, Justin, Rostkowski, Pawel, Rüdel, Heinz, Salek, Reza M., Samanipour, Saer, Scheringer, Martin, Schliebner, Ivo, Schulz, Wolfgang, Schulze, Tobias, Sengl, Manfred, Shoemaker, Benjamin A., Sims, Kerry, Singer, Heinz, Singh, Randolph R., Sumarah, Mark, Thiessen, Paul A., Thomas, Kevin V., Torres, Sonia, Trier, Xenia, van Wezel, Annemarie P., Vermeulen, Roel C. H., Vlaanderen, Jelle J., von der Ohe, Peter C., Wang, Zhanyun, Williams, Antony J., Willighagen, Egon L., Wishart, David S., Zhang, Jian, Thomaidis, Nikolaos S., Hollender, Juliane, Slobodnik, Jaroslav, Schymanski, Emma L., Taha, Hiba Mohammed, Aalizadeh, Reza, Alygizakis, Nikiforos, Antignac, Jean-Philippe, Arp, Hans Peter H., Bade, Richard, Baker, Nancy, Belova, Lidia, Bijlsma, Lubertus, Bolton, Evan E., Brack, Werner, Celma, Alberto, Chen, Wen-Ling, Cheng, Tiejun, Chirsir, Parviel, Čirka, Ľuboš, D'Agostino, Lisa A., Feunang, Yannick Djoumbou, Dulio, Valeria, Fischer, Stellan, Gago-Ferrero, Pablo, Galani, Aikaterini, Geueke, Birgit, Głowacka, Natalia, Glüge, Juliane, Groh, Ksenia, Grosse, Sylvia, Haglund, Peter, Hakkinen, Pertti J., Hale, Sarah E., Hernandez, Felix, Janssen, Elisabeth M.-L., Jonkers, Tim, Kiefer, Karin, Kirchner, Michal, Koschorreck, Jan, Krauss, Martin, Krier, Jessy, Lamoree, Marja H., Letzel, Marion, Letzel, Thomas, Li, Qingliang, Little, James, Liu, Yanna, Lunderberg, David M., Martin, Jonathan W., McEachran, Andrew D., McLean, John A., Meier, Christiane, Meijer, Jeroen, Menger, Frank, Merino, Carla, Muncke, Jane, Muschket, Matthias, Neumann, Michael, Neveu, Vanessa, Ng, Kelsey, Oberacher, Herbert, O'Brien, Jake, Oswald, Peter, Oswaldova, Martina, Picache, Jaqueline A., Postigo, Cristina, Ramirez, Noelia, Reemtsma, Thorsten, Renaud, Justin, Rostkowski, Pawel, Rüdel, Heinz, Salek, Reza M., Samanipour, Saer, Scheringer, Martin, Schliebner, Ivo, Schulz, Wolfgang, Schulze, Tobias, Sengl, Manfred, Shoemaker, Benjamin A., Sims, Kerry, Singer, Heinz, Singh, Randolph R., Sumarah, Mark, Thiessen, Paul A., Thomas, Kevin V., Torres, Sonia, Trier, Xenia, van Wezel, Annemarie P., Vermeulen, Roel C. H., Vlaanderen, Jelle J., von der Ohe, Peter C., Wang, Zhanyun, Williams, Antony J., Willighagen, Egon L., Wishart, David S., Zhang, Jian, Thomaidis, Nikolaos S., Hollender, Juliane, Slobodnik, Jaroslav, and Schymanski, Emma L.

Abstract

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

Published
2022
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39. Studying the Parkinson's disease metabolome and exposome in biological samples through different analytical and cheminformatics approaches: a pilot study

Author

Luxembourg Centre for Systems Biomedicine (LCSB): Environmental Cheminformatics (Schymanski Group) [research center], Luxembourg Centre for Systems Biomedicine (LCSB): Eco-Systems Biology (Wilmes Group) [research center], Talavera Andujar, Begona, Aurich, Dagny, Aho, Velma, Singh, Randolph R., Cheng, Tiejun, Zaslavsky, Leonid, Bolton, Evan E., Mollenhauer, Brit, Wilmes, Paul, Schymanski, Emma, Luxembourg Centre for Systems Biomedicine (LCSB): Environmental Cheminformatics (Schymanski Group) [research center], Luxembourg Centre for Systems Biomedicine (LCSB): Eco-Systems Biology (Wilmes Group) [research center], Talavera Andujar, Begona, Aurich, Dagny, Aho, Velma, Singh, Randolph R., Cheng, Tiejun, Zaslavsky, Leonid, Bolton, Evan E., Mollenhauer, Brit, Wilmes, Paul, and Schymanski, Emma

Abstract

Parkinson’s disease (PD) is the second most prevalent neurodegenerative disease, with an increasing incidence in recent years due to the ageing population. Genetic mutations alone only explain <10% of PD cases, while environmental factors, including small molecules, may play a significant role in PD. In the present work, 22 plasma (11 PD, 11 control) and 19 feces samples (10 PD, 9 control) were analyzed by non-target high resolution mass spectrometry (NT-HRMS) coupled to two liquid chromatography (LC) methods (reversed phase (RP) and hydrophilic interaction liquid chromatography (HILIC)). A cheminformatics workflow was optimized using open software (MS-DIAL and patRoon) and open databases (all public MSP-formatted spectral libraries for MS-DIAL, PubChemLite for Exposomics and the LITMINEDNEURO list for patRoon). Furthermore, five disease-specific databases and three suspect lists (on PD and related disorders) were developed, using PubChem functionality to identifying relevant unknown chemicals. The results showed that non-target screening with the larger databases generally provided better results compared with smaller suspect lists. However, two suspect screening approaches with patRoon were also good options to study specific chemicals in PD. The combination of chromatographic methods (RP and HILIC) as well as two ionization modes (positive and negative) enhanced the coverage of chemicals in the biological samples. While most metabolomics studies in PD have focused on blood and cerebrospinal fluid, we found a higher number of relevant features in feces, such as alanine betaine or nicotinamide, which can be directly metabolized by gut microbiota. This highlights the potential role of gut dysbiosis in PD development.

Published
2022

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

Author

IRAS OH Epidemiology Chemical Agents, Mohammed Taha, Hiba, Aalizadeh, Reza, Alygizakis, Nikiforos, Antignac, Jean-Philippe, Arp, Hans Peter H, Bade, Richard, Baker, Nancy, Belova, Lidia, Bijlsma, Lubertus, Bolton, Evan E, Brack, Werner, Celma, Alberto, Chen, Wen-Ling, Cheng, Tiejun, Chirsir, Parviel, Čirka, Ľuboš, D'Agostino, Lisa A, Djoumbou Feunang, Yannick, Dulio, Valeria, Fischer, Stellan, Gago-Ferrero, Pablo, Galani, Aikaterini, Geueke, Birgit, Głowacka, Natalia, Glüge, Juliane, Groh, Ksenia, Grosse, Sylvia, Haglund, Peter, Hakkinen, Pertti J, Hale, Sarah E, Hernandez, Felix, Janssen, Elisabeth M-L, Jonkers, Tim, Kiefer, Karin, Kirchner, Michal, Koschorreck, Jan, Krauss, Martin, Krier, Jessy, Lamoree, Marja H, Letzel, Marion, Letzel, Thomas, Li, Qingliang, Little, James, Liu, Yanna, Lunderberg, David M, Martin, Jonathan W, McEachran, Andrew D, McLean, John A, Meier, Christiane, Meijer, Jeroen, Menger, Frank, Merino, Carla, Muncke, Jane, Muschket, Matthias, Neumann, Michael, Neveu, Vanessa, Ng, Kelsey, Oberacher, Herbert, O'Brien, Jake, Oswald, Peter, Oswaldova, Martina, Picache, Jaqueline A, Postigo, Cristina, Ramirez, Noelia, Reemtsma, Thorsten, Renaud, Justin, Rostkowski, Pawel, Rüdel, Heinz, Salek, Reza M, Samanipour, Saer, Scheringer, Martin, Schliebner, Ivo, Schulz, Wolfgang, Schulze, Tobias, Sengl, Manfred, Shoemaker, Benjamin A, Sims, Kerry, Singer, Heinz, Singh, Randolph R, Sumarah, Mark, Thiessen, Paul A, Thomas, Kevin V, Torres, Sonia, Trier, Xenia, van Wezel, Annemarie P, Vermeulen, Roel C H, Vlaanderen, Jelle J, von der Ohe, Peter C, Wang, Zhanyun, Williams, Antony J, Willighagen, Egon L, Wishart, David S, Zhang, Jian, Thomaidis, Nikolaos S, Hollender, Juliane, Slobodnik, Jaroslav, Schymanski, Emma L, IRAS OH Epidemiology Chemical Agents, Mohammed Taha, Hiba, Aalizadeh, Reza, Alygizakis, Nikiforos, Antignac, Jean-Philippe, Arp, Hans Peter H, Bade, Richard, Baker, Nancy, Belova, Lidia, Bijlsma, Lubertus, Bolton, Evan E, Brack, Werner, Celma, Alberto, Chen, Wen-Ling, Cheng, Tiejun, Chirsir, Parviel, Čirka, Ľuboš, D'Agostino, Lisa A, Djoumbou Feunang, Yannick, Dulio, Valeria, Fischer, Stellan, Gago-Ferrero, Pablo, Galani, Aikaterini, Geueke, Birgit, Głowacka, Natalia, Glüge, Juliane, Groh, Ksenia, Grosse, Sylvia, Haglund, Peter, Hakkinen, Pertti J, Hale, Sarah E, Hernandez, Felix, Janssen, Elisabeth M-L, Jonkers, Tim, Kiefer, Karin, Kirchner, Michal, Koschorreck, Jan, Krauss, Martin, Krier, Jessy, Lamoree, Marja H, Letzel, Marion, Letzel, Thomas, Li, Qingliang, Little, James, Liu, Yanna, Lunderberg, David M, Martin, Jonathan W, McEachran, Andrew D, McLean, John A, Meier, Christiane, Meijer, Jeroen, Menger, Frank, Merino, Carla, Muncke, Jane, Muschket, Matthias, Neumann, Michael, Neveu, Vanessa, Ng, Kelsey, Oberacher, Herbert, O'Brien, Jake, Oswald, Peter, Oswaldova, Martina, Picache, Jaqueline A, Postigo, Cristina, Ramirez, Noelia, Reemtsma, Thorsten, Renaud, Justin, Rostkowski, Pawel, Rüdel, Heinz, Salek, Reza M, Samanipour, Saer, Scheringer, Martin, Schliebner, Ivo, Schulz, Wolfgang, Schulze, Tobias, Sengl, Manfred, Shoemaker, Benjamin A, Sims, Kerry, Singer, Heinz, Singh, Randolph R, Sumarah, Mark, Thiessen, Paul A, Thomas, Kevin V, Torres, Sonia, Trier, Xenia, van Wezel, Annemarie P, Vermeulen, Roel C H, Vlaanderen, Jelle J, von der Ohe, Peter C, Wang, Zhanyun, Williams, Antony J, Willighagen, Egon L, Wishart, David S, Zhang, Jian, Thomaidis, Nikolaos S, Hollender, Juliane, Slobodnik, Jaroslav, and Schymanski, Emma L

Published
2022

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

Author

Mohammed Taha, Hiba, Aalizadeh, Reza, Alygizakis, Nikiforos, Antignac, Jean Philippe, Arp, Hans Peter H., Bade, Richard, Baker, Nancy, Belova, Lidia, Bijlsma, Lubertus, Bolton, Evan E., Brack, Werner, Celma, Alberto, Chen, Wen Ling, Cheng, Tiejun, Chirsir, Parviel, Čirka, Ľuboš, D’Agostino, Lisa A., Djoumbou Feunang, Yannick, Dulio, Valeria, Fischer, Stellan, Gago-Ferrero, Pablo, Galani, Aikaterini, Geueke, Birgit, Głowacka, Natalia, Glüge, Juliane, Groh, Ksenia, Grosse, Sylvia, Haglund, Peter, Hakkinen, Pertti J., Hale, Sarah E., Hernandez, Felix, Janssen, Elisabeth M.L., Jonkers, Tim, Kiefer, Karin, Kirchner, Michal, Koschorreck, Jan, Krauss, Martin, Krier, Jessy, Lamoree, Marja H., Letzel, Marion, Letzel, Thomas, Li, Qingliang, Little, James, Liu, Yanna, Lunderberg, David M., Martin, Jonathan W., McEachran, Andrew D., McLean, John A., Meier, Christiane, Meijer, Jeroen, Menger, Frank, Merino, Carla, Muncke, Jane, Muschket, Matthias, Neumann, Michael, Neveu, Vanessa, Ng, Kelsey, Oberacher, Herbert, O’Brien, Jake, Oswald, Peter, Oswaldova, Martina, Picache, Jaqueline A., Postigo, Cristina, Ramirez, Noelia, Reemtsma, Thorsten, Renaud, Justin, Rostkowski, Pawel, Rüdel, Heinz, Salek, Reza M., Samanipour, Saer, Scheringer, Martin, Schliebner, Ivo, Schulz, Wolfgang, Schulze, Tobias, Sengl, Manfred, Shoemaker, Benjamin A., Sims, Kerry, Singer, Heinz, Singh, Randolph R., Sumarah, Mark, Thiessen, Paul A., Thomas, Kevin V., Torres, Sonia, Trier, Xenia, van Wezel, Annemarie P., Vermeulen, Roel C.H., Vlaanderen, Jelle J., von der Ohe, Peter C., Wang, Zhanyun, Williams, Antony J., Willighagen, Egon L., Wishart, David S., Zhang, Jian, Thomaidis, Nikolaos S., Hollender, Juliane, Slobodnik, Jaroslav, Schymanski, Emma L., Mohammed Taha, Hiba, Aalizadeh, Reza, Alygizakis, Nikiforos, Antignac, Jean Philippe, Arp, Hans Peter H., Bade, Richard, Baker, Nancy, Belova, Lidia, Bijlsma, Lubertus, Bolton, Evan E., Brack, Werner, Celma, Alberto, Chen, Wen Ling, Cheng, Tiejun, Chirsir, Parviel, Čirka, Ľuboš, D’Agostino, Lisa A., Djoumbou Feunang, Yannick, Dulio, Valeria, Fischer, Stellan, Gago-Ferrero, Pablo, Galani, Aikaterini, Geueke, Birgit, Głowacka, Natalia, Glüge, Juliane, Groh, Ksenia, Grosse, Sylvia, Haglund, Peter, Hakkinen, Pertti J., Hale, Sarah E., Hernandez, Felix, Janssen, Elisabeth M.L., Jonkers, Tim, Kiefer, Karin, Kirchner, Michal, Koschorreck, Jan, Krauss, Martin, Krier, Jessy, Lamoree, Marja H., Letzel, Marion, Letzel, Thomas, Li, Qingliang, Little, James, Liu, Yanna, Lunderberg, David M., Martin, Jonathan W., McEachran, Andrew D., McLean, John A., Meier, Christiane, Meijer, Jeroen, Menger, Frank, Merino, Carla, Muncke, Jane, Muschket, Matthias, Neumann, Michael, Neveu, Vanessa, Ng, Kelsey, Oberacher, Herbert, O’Brien, Jake, Oswald, Peter, Oswaldova, Martina, Picache, Jaqueline A., Postigo, Cristina, Ramirez, Noelia, Reemtsma, Thorsten, Renaud, Justin, Rostkowski, Pawel, Rüdel, Heinz, Salek, Reza M., Samanipour, Saer, Scheringer, Martin, Schliebner, Ivo, Schulz, Wolfgang, Schulze, Tobias, Sengl, Manfred, Shoemaker, Benjamin A., Sims, Kerry, Singer, Heinz, Singh, Randolph R., Sumarah, Mark, Thiessen, Paul A., Thomas, Kevin V., Torres, Sonia, Trier, Xenia, van Wezel, Annemarie P., Vermeulen, Roel C.H., Vlaanderen, Jelle J., von der Ohe, Peter C., Wang, Zhanyun, Williams, Antony J., Willighagen, Egon L., Wishart, David S., Zhang, Jian, Thomaidis, Nikolaos S., Hollender, Juliane, Slobodnik, Jaroslav, and Schymanski, Emma L.

Abstract

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.

Published
2022

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

Author

Ministerio de Ciencia e Innovación (España), European Commission, 0000-0001-7820-4335, 0000-0001-9167-9060, 0000-0002-5727-4999, 0000-0001-9512-9314, 0000-0002-0747-8838, 0000-0003-2724-9183, 0000-0002-8351-9435, 0000-0001-7147-384X, 0000-0001-7005-8775, 0000-0002-5959-6190, 0000-0001-9269-6524, 0000-0001-9763-8737, 0000-0001-5143-0543, 0000-0002-4486-3356, 0000-0002-9932-8609, 0000-0001-9351-6855, 0000-0002-9734-324X, 0000-0001-7850-184X, 0000-0002-9436-9954, 0000-0002-5987-0399, 0000-0003-1112-6867, 0000-0002-0749-3982, 0000-0002-1740-9422, 0000-0003-1997-2750, 0000-0002-3778-4721, 0000-0003-2293-7913, 0000-0002-8295-9738, 0000-0002-7743-9199, 0000-0003-1268-3083, 0000-0002-5475-6730, 0000-0002-6415-6173, 0000-0002-6917-3431, 0000-0002-1043-3278, 0000-0002-0362-4244, 0000-0001-6986-5545, 0000-0002-7373-7738, 0000-0003-1008-8790, 0000-0002-6453-236X, 0000-0001-7893-9876, 0000-0002-4439-9194, 0000-0001-6265-4294, 0000-0003-1423-330X, 0000-0001-8918-6419, 0000-0003-3126-5186, 0000-0002-4551-6823, 0000-0002-1808-8835, 0000-0002-8793-5516, 0000-0002-6942-0594, 0000-0001-6672-8414, 0000-0002-2558-4431, 0000-0002-8501-7789, 0000-0003-2396-2993, 0000-0002-0963-8268, 0000-0001-9336-9656, 0000-0003-3088-9771, 0000-0002-1948-9243, 0000-0002-7344-7044, 0000-0002-9251-0790, 0000-0003-1606-0764, 0000-0001-6974-0224, 0000-0001-9778-4283, 0000-0002-4175-4787, 0000-0001-8604-1732, 0000-0001-8270-6979, 0000-0002-0809-7826, 0000-0002-1553-3868, 0000-0002-9744-8914, 0000-0002-1356-285X, 0000-0001-6273-4083, 0000-0002-8542-3699, 0000-0003-4500-3400, 0000-0003-0977-1656, 0000-0002-1992-2086, 0000-0002-2155-100X, 0000-0001-8881-0793, 0000-0001-6067-8321, 0000-0002-6875-957X, 0000-0003-4082-8163, 0000-0001-7350-8962, 0000-0001-9914-7659, 0000-0002-2668-4821, 0000-0001-7542-0286, 0000-0002-3207-2434, 0000-0002-6192-4632, 0000-0002-4624-4735, 0000-0002-4660-274X, 0000-0003-2622-6318, 0000-0001-6868-8145, Mohammed Taha, Hiba, Aalizadeh, Reza, Alygizakis, Nikiforos, Antignac, Jean-Philippe, Arp, Hans Peter H., Bade, Richard, Baker, Nancy, Belova, Lidia, Bijlsma, Lubertus, Bolton, Evan E., Brack, Werner, Celma, Alberto, Chen, Wen-Ling, Cheng, Tiejun, Chirsir, Parviel, Čirka, Ľuboš, D'Agostino, Lisa A., Djoumbou Feunang, Yannick, Dulio, Valeria, Fischer, Stellan, Gago-Ferrero, Pablo, Galani, Aikaterini, Geueke, Birgit, Głowacka, Natalia, Glüge, Juliane, Groh, Ksenia, Grosse, Sylvia, Haglund, Peter, Hakkinen, Pertti J., Hale, Sarah E., Hernandez, Felix, Janssen, Elisabeth M-L., Jonkers, Tim, Kiefer, Karin, Kirchner, Michal, Koschorreck, Jan, Krauss, Martin, Krier, Jessy, Lamoree, Marja H., Letzel, Marion, Letzel, Thomas, Li, Qingliang, Little, James, Liu, Yanna, Lunderberg, David M., Martin, Jonathan W., McEachran, Andrew D., McLean, John A., Meier, Christiane, Meijer, Jeroen, Menger, Frank, Merino, Carla, Muncke, Jane, Muschket, Matthias, Neumann, Michael, Neveu, Vanessa, Ng, Kelsey, Oberacher, Herbert, O'Brien, Jake, Oswald, Peter, Oswaldova, Martina, Picache, Jaqueline A., Postigo, Cristina, Ramírez, Noelia, Reemtsma, Thorsten, Renaud, Justin, Rostkowski, Pawel, Rüdel, Heinz, Salek, Reza M., Samanipour, Saer, Scheringer, Martin, Schliebner, Ivo, Schulz, Wolfgang, Schulze, Tobias, Sengl, Manfred, Shoemaker, Benjamin A., Sims, Kerry, Singer, Heinz, Singh, Randolph R., Sumarah, Mark, Thiessen, Paul A., Thomas, Kevin V., Torres, Sonia, Trier, Xenia, van Wezel, Annemarie P., Vermeulen, Roel C. H., Vlaanderen, Jelle J., von der Ohe, Peter C., Wang, Zhanyun, Williams, Antony J., Willighagen, Egon L., Wishart, David S., Zhang, Jian, Thomaidis, Nikolaos S., Hollender, Juliane, Slobodnik, Jaroslav, Schymanski, Emma L., Ministerio de Ciencia e Innovación (España), European Commission, 0000-0001-7820-4335, 0000-0001-9167-9060, 0000-0002-5727-4999, 0000-0001-9512-9314, 0000-0002-0747-8838, 0000-0003-2724-9183, 0000-0002-8351-9435, 0000-0001-7147-384X, 0000-0001-7005-8775, 0000-0002-5959-6190, 0000-0001-9269-6524, 0000-0001-9763-8737, 0000-0001-5143-0543, 0000-0002-4486-3356, 0000-0002-9932-8609, 0000-0001-9351-6855, 0000-0002-9734-324X, 0000-0001-7850-184X, 0000-0002-9436-9954, 0000-0002-5987-0399, 0000-0003-1112-6867, 0000-0002-0749-3982, 0000-0002-1740-9422, 0000-0003-1997-2750, 0000-0002-3778-4721, 0000-0003-2293-7913, 0000-0002-8295-9738, 0000-0002-7743-9199, 0000-0003-1268-3083, 0000-0002-5475-6730, 0000-0002-6415-6173, 0000-0002-6917-3431, 0000-0002-1043-3278, 0000-0002-0362-4244, 0000-0001-6986-5545, 0000-0002-7373-7738, 0000-0003-1008-8790, 0000-0002-6453-236X, 0000-0001-7893-9876, 0000-0002-4439-9194, 0000-0001-6265-4294, 0000-0003-1423-330X, 0000-0001-8918-6419, 0000-0003-3126-5186, 0000-0002-4551-6823, 0000-0002-1808-8835, 0000-0002-8793-5516, 0000-0002-6942-0594, 0000-0001-6672-8414, 0000-0002-2558-4431, 0000-0002-8501-7789, 0000-0003-2396-2993, 0000-0002-0963-8268, 0000-0001-9336-9656, 0000-0003-3088-9771, 0000-0002-1948-9243, 0000-0002-7344-7044, 0000-0002-9251-0790, 0000-0003-1606-0764, 0000-0001-6974-0224, 0000-0001-9778-4283, 0000-0002-4175-4787, 0000-0001-8604-1732, 0000-0001-8270-6979, 0000-0002-0809-7826, 0000-0002-1553-3868, 0000-0002-9744-8914, 0000-0002-1356-285X, 0000-0001-6273-4083, 0000-0002-8542-3699, 0000-0003-4500-3400, 0000-0003-0977-1656, 0000-0002-1992-2086, 0000-0002-2155-100X, 0000-0001-8881-0793, 0000-0001-6067-8321, 0000-0002-6875-957X, 0000-0003-4082-8163, 0000-0001-7350-8962, 0000-0001-9914-7659, 0000-0002-2668-4821, 0000-0001-7542-0286, 0000-0002-3207-2434, 0000-0002-6192-4632, 0000-0002-4624-4735, 0000-0002-4660-274X, 0000-0003-2622-6318, 0000-0001-6868-8145, Mohammed Taha, Hiba, Aalizadeh, Reza, Alygizakis, Nikiforos, Antignac, Jean-Philippe, Arp, Hans Peter H., Bade, Richard, Baker, Nancy, Belova, Lidia, Bijlsma, Lubertus, Bolton, Evan E., Brack, Werner, Celma, Alberto, Chen, Wen-Ling, Cheng, Tiejun, Chirsir, Parviel, Čirka, Ľuboš, D'Agostino, Lisa A., Djoumbou Feunang, Yannick, Dulio, Valeria, Fischer, Stellan, Gago-Ferrero, Pablo, Galani, Aikaterini, Geueke, Birgit, Głowacka, Natalia, Glüge, Juliane, Groh, Ksenia, Grosse, Sylvia, Haglund, Peter, Hakkinen, Pertti J., Hale, Sarah E., Hernandez, Felix, Janssen, Elisabeth M-L., Jonkers, Tim, Kiefer, Karin, Kirchner, Michal, Koschorreck, Jan, Krauss, Martin, Krier, Jessy, Lamoree, Marja H., Letzel, Marion, Letzel, Thomas, Li, Qingliang, Little, James, Liu, Yanna, Lunderberg, David M., Martin, Jonathan W., McEachran, Andrew D., McLean, John A., Meier, Christiane, Meijer, Jeroen, Menger, Frank, Merino, Carla, Muncke, Jane, Muschket, Matthias, Neumann, Michael, Neveu, Vanessa, Ng, Kelsey, Oberacher, Herbert, O'Brien, Jake, Oswald, Peter, Oswaldova, Martina, Picache, Jaqueline A., Postigo, Cristina, Ramírez, Noelia, Reemtsma, Thorsten, Renaud, Justin, Rostkowski, Pawel, Rüdel, Heinz, Salek, Reza M., Samanipour, Saer, Scheringer, Martin, Schliebner, Ivo, Schulz, Wolfgang, Schulze, Tobias, Sengl, Manfred, Shoemaker, Benjamin A., Sims, Kerry, Singer, Heinz, Singh, Randolph R., Sumarah, Mark, Thiessen, Paul A., Thomas, Kevin V., Torres, Sonia, Trier, Xenia, van Wezel, Annemarie P., Vermeulen, Roel C. H., Vlaanderen, Jelle J., von der Ohe, Peter C., Wang, Zhanyun, Williams, Antony J., Willighagen, Egon L., Wishart, David S., Zhang, Jian, Thomaidis, Nikolaos S., Hollender, Juliane, Slobodnik, Jaroslav, and Schymanski, Emma L.

Abstract

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.

Published
2022

43. Additional file 2 of The NORMAN Suspect List Exchange (NORMAN-SLE): facilitating European and worldwide collaboration on suspect screening in high resolution mass spectrometry

Author

Mohammed Taha, Hiba, Aalizadeh, Reza, Alygizakis, Nikiforos, Antignac, Jean-Philippe, Arp, Hans Peter H., Bade, Richard, Baker, Nancy, Belova, Lidia, Bijlsma, Lubertus, Bolton, Evan E., Brack, Werner, Celma, Alberto, Chen, Wen-Ling, Cheng, Tiejun, Chirsir, Parviel, Čirka, Ľuboš, D’Agostino, Lisa A., Djoumbou Feunang, Yannick, Dulio, Valeria, Fischer, Stellan, Gago-Ferrero, Pablo, Galani, Aikaterini, Geueke, Birgit, Głowacka, Natalia, Glüge, Juliane, Groh, Ksenia, Grosse, Sylvia, Haglund, Peter, Hakkinen, Pertti J., Hale, Sarah E., Hernandez, Felix, Janssen, Elisabeth M.-L., Jonkers, Tim, Kiefer, Karin, Kirchner, Michal, Koschorreck, Jan, Krauss, Martin, Krier, Jessy, Lamoree, Marja H., Letzel, Marion, Letzel, Thomas, Li, Qingliang, Little, James, Liu, Yanna, Lunderberg, David M., Martin, Jonathan W., McEachran, Andrew D., McLean, John A., Meier, Christiane, Meijer, Jeroen, Menger, Frank, Merino, Carla, Muncke, Jane, Muschket, Matthias, Neumann, Michael, Neveu, Vanessa, Ng, Kelsey, Oberacher, Herbert, O’Brien, Jake, Oswald, Peter, Oswaldova, Martina, Picache, Jaqueline A., Postigo, Cristina, Ramirez, Noelia, Reemtsma, Thorsten, Renaud, Justin, Rostkowski, Pawel, Rüdel, Heinz, Salek, Reza M., Samanipour, Saer, Scheringer, Martin, Schliebner, Ivo, Schulz, Wolfgang, Schulze, Tobias, Sengl, Manfred, Shoemaker, Benjamin A., Sims, Kerry, Singer, Heinz, Singh, Randolph R., Sumarah, Mark, Thiessen, Paul A., Thomas, Kevin V., Torres, Sonia, Trier, Xenia, van Wezel, Annemarie P., Vermeulen, Roel C. H., Vlaanderen, Jelle J., von der Ohe, Peter C., Wang, Zhanyun, Williams, Antony J., Willighagen, Egon L., Wishart, David S., Zhang, Jian, Thomaidis, Nikolaos S., Hollender, Juliane, Slobodnik, Jaroslav, and Schymanski, Emma L.

Subjects
Pharmacology, Ecology, 39999 Chemical Sciences not elsewhere classified, FOS: Chemical sciences, FOS: Biological sciences, Computational Biology, Marine Biology, Biochemistry, Molecular Biology, Biotechnology, Cancer
Abstract

Additional file 2: Overview of the NORMAN-SLE website (DOCX format) as of 30 May 2022 [82].

Published
2022
Full Text
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44. Open access chemical information integration in PubChem

Author

Zhang, Jiangyang and Bolton, Evan E.

Abstract

PubChem (https://pubchem.ncbi.nlm.nih.gov/) is an open chemistry database within the National Library of Medicine at the National Institutes of Health. PubChem has served the community since 2004. Today, PubChem provides information for more than 110 million unique compounds that link to nearly 300 million bioactivities, 42 million patents, and 34 million literatures. With such massive information, PubChem serves millions of users that yield more than 10 million page views per month. As an information hub, PubChem integrates chemical data from more than 860 data sources around the world. In this presentation, we will discuss the chemical data integration from open access databases including EPA, FDA, USDA, ATSDR, NIOSH, USGS, ECHA, WHO, FAO, ILO, EMA, and more. We will also discuss the challenges for data mapping and standardization. Lastly, we will present the data retrieving tools using PubChem's restful APIs and classification browser.

Published
2022
Full Text
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46. [Preprint] Letter to the Editor: FAIR-ifying the Exposome: Chemical Structures and Transformations

Author

Schymanski, Emma L. and Bolton, Evan E.

Subjects
chemical information, data sharing, open science, transformation products, data workflows, FAIR
Abstract

The start of our conversation with the Exposome Journal about FAIRifying the Exposome with data templates, developing the ideas for FAIR chemical structures presented recently in the Journal of Cheminfomatics (here) further. Uploaded with permission by the EiC, Gary W. Miller. Interestingly, other preprint servers don't seem to readily accept commentaries or letters ... hence depositing here! Feedback and contributions using these templates very welcome!, Preprint of the version submitted to the journal September 7th, 2021

Published
2021
Full Text
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48. Database resources of the national center for biotechnology information

Author

Sayers, Eric W, primary, Bolton, Evan E, additional, Brister, J Rodney, additional, Canese, Kathi, additional, Chan, Jessica, additional, Comeau, Donald C, additional, Connor, Ryan, additional, Funk, Kathryn, additional, Kelly, Chris, additional, Kim, Sunghwan, additional, Madej, Tom, additional, Marchler-Bauer, Aron, additional, Lanczycki, Christopher, additional, Lathrop, Stacy, additional, Lu, Zhiyong, additional, Thibaud-Nissen, Francoise, additional, Murphy, Terence, additional, Phan, Lon, additional, Skripchenko, Yuri, additional, Tse, Tony, additional, Wang, Jiyao, additional, Williams, Rebecca, additional, Trawick, Barton W, additional, Pruitt, Kim D, additional, and Sherry, Stephen T, additional

Published
2021
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49. PubChem 2023 update.

Author

Kim, Sunghwan, Chen, Jie, Cheng, Tiejun, Gindulyte, Asta, He, Jia, He, Siqian, Li, Qingliang, Shoemaker, Benjamin A, Thiessen, Paul A, Yu, Bo, Zaslavsky, Leonid, Zhang, Jian, and Bolton, Evan E

Published
2023
Full Text
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50. FAIR chemical structures in the Journal of Cheminformatics

Author

Schymanski, Emma, Bolton, Evan E., and Fonds National de la Recherche - FnR [sponsor]

Subjects
Chemistry [G01] [Physical, chemical, mathematical & earth Sciences], Chimie [G01] [Physique, chimie, mathématiques & sciences de la terre]
Abstract

The ability to access chemical information openly is an essential part of many scientific disciplines. The Journal of Cheminformatics is leading the way for rigorous, open cheminformatics in many ways, but there remains room for improvement in primary areas. This letter discusses how both authors and the journal alike can help increase the FAIR ness (Findability, Accessibility, Interoperability, Reusability) of the chemical structural information in the journal. A proposed chemical structure template can serve as an interoperable Additional File format (already accessible ), made more findable by linking the DOI of this data file to the article DOI metadata, supporting further reuse .

Published
2021

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