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228 results on '"Willighagen, Egon L"'

1. Artificial intelligence for natural product drug discovery

Author

Mullowney, Michael W., Duncan, Katherine R., Elsayed, Somayah S., Garg, Neha, van der Hooft, Justin J. J., Martin, Nathaniel I., Meijer, David, Terlouw, Barbara R., Biermann, Friederike, Blin, Kai, Durairaj, Janani, Gorostiola González, Marina, Helfrich, Eric J. N., Huber, Florian, Leopold-Messer, Stefan, Rajan, Kohulan, de Rond, Tristan, van Santen, Jeffrey A., Sorokina, Maria, Balunas, Marcy J., Beniddir, Mehdi A., van Bergeijk, Doris A., Carroll, Laura M., Clark, Chase M., Clevert, Djork-Arné, Dejong, Chris A., Du, Chao, Ferrinho, Scarlet, Grisoni, Francesca, Hofstetter, Albert, Jespers, Willem, Kalinina, Olga V., Kautsar, Satria A., Kim, Hyunwoo, Leao, Tiago F., Masschelein, Joleen, Rees, Evan R., Reher, Raphael, Reker, Daniel, Schwaller, Philippe, Segler, Marwin, Skinnider, Michael A., Walker, Allison S., Willighagen, Egon L., Zdrazil, Barbara, Ziemert, Nadine, Goss, Rebecca J. M., Guyomard, Pierre, Volkamer, Andrea, Gerwick, William H., Kim, Hyun Uk, Müller, Rolf, van Wezel, Gilles P., van Westen, Gerard J. P., Hirsch, Anna K. H., Linington, Roger G., Robinson, Serina L., and Medema, Marnix H.

Published
2023
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4. Guiding the choice of informatics software and tools for lipidomics research applications

Author

Ni, Zhixu, Wölk, Michele, Jukes, Geoff, Mendivelso Espinosa, Karla, Ahrends, Robert, Aimo, Lucila, Alvarez-Jarreta, Jorge, Andrews, Simon, Andrews, Robert, Bridge, Alan, Clair, Geremy C., Conroy, Matthew J., Fahy, Eoin, Gaud, Caroline, Goracci, Laura, Hartler, Jürgen, Hoffmann, Nils, Kopczyinki, Dominik, Korf, Ansgar, Lopez-Clavijo, Andrea F., Malik, Adnan, Ackerman, Jacobo Miranda, Molenaar, Martijn R., O’Donovan, Claire, Pluskal, Tomáš, Shevchenko, Andrej, Slenter, Denise, Siuzdak, Gary, Kutmon, Martina, Tsugawa, Hiroshi, Willighagen, Egon L., Xia, Jianguo, O’Donnell, Valerie B., and Fedorova, Maria

Published
2023
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5. A template wizard for the cocreation of machine-readable data-reporting to harmonize the evaluation of (nano)materials

Author

European Commission, Slovenian Research Agency, Norwegian Research Council, Jeliazkova, Nina [0000-0002-4322-6179], Longhin, Eleonora [0000-0002-3939-7135], El Yamani, Naouale [0000-0001-5456-8230], Rundén-Pran, Elise [0000-0002-5541-4513], Moschini, Elisa [0000-0001-9825-6263], Serchi, Tommaso [0000-0003-2386-3514], Vrček, Ivana Vinković [0000-0003-1382-5581], Burgum, Michael J. [0000-0002-3123-8914], Doak, Shareen H. [0000-0002-6753-1987], Cimpan, Mihaela Roxana [0000-0003-2029-3173], Battistelli, Chiara [0000-0003-2386-0727], Bossa, Cecilia [0000-0003-2084-2902], Tsekovska, Rositsa [0000-0001-5431-5743], Drobne, Damjana [0000-0002-5970-7460], Novak, Sara [0000-0003-0026-456X], Repar, Neža [0000-0003-4310-0362], Ammar, Ammar [0000-0002-8399-8990], Nymark, Penny [0000-0002-3435-7775], Di Battista, Veronica [0000-0002-6491-9185], Sosnowska, Anita [0000-0003-3288-4309], Puzyn, Tomasz [0000-0003-0449-8339], Kochev, Nikolay [0000-0001-6547-3675], Iliev, Luchesar [0000-0001-7000-8890], Jeliazkov, Vedrin [0000-0002-1520-5995], Reilly, Katie [0000-0002-6054-0645], Lynch, Iseult [0000-0003-4250-4584], Bakker, Martine [0000-0001-8379-7016], Delpivo, Camila [0000-0002-4413-7602], Sánchez-Jiménez, A. [0000-0002-2625-9155], Fonseca, Ana Sofia [0000-0002-1424-6365], Manier, Nicolas [0000-0003-3873-6657], Fernández-Cruz, M. L. [0000-0001-5988-1939], Rashid, Shahzad [0009-0002-3525-6607], Willighagen, Egon L. [0000-0001-7542-0286], Apostolova, Margarita D. [0000-0001-7188-506X], Dusinska, Maria [0000-0003-1358-1652], Jeliazkova, Nina, Longhin, Eleonora, El Yamani, Naouale, Rundén-Pran, Elise, Moschini, Elisa, Serchi, Tommaso, Vrček, Ivana Vinković, Burgum, Michael J., Doak, Shareen H., Cimpan, Mihaela Roxana, Rios-Mondragon, Ivan, Cimpan, Emil, Battistelli, Chiara, Bossa, Cecilia, Tsekovska, Rositsa, Drobne, Damjana, Novak, Sara, Repar, Neža, Ammar, Ammar, Nymark, Penny, Di Battista, Veronica, Sosnowska, Anita, Puzyn, Tomasz, Kochev, Nikolay, Iliev, Luchesar, Jeliazkov, Vedrin, Reilly, Katie, Lynch, Iseult, Bakker, Martine, Delpivo, Camila, Sánchez-Jiménez, A., Fonseca, Ana Sofia, Manier, Nicolas, Fernández-Cruz, M. L., Rashid, Shahzad, Willighagen, Egon L., Apostolova, Margarita D., Dusinska, Maria, European Commission, Slovenian Research Agency, Norwegian Research Council, Jeliazkova, Nina [0000-0002-4322-6179], Longhin, Eleonora [0000-0002-3939-7135], El Yamani, Naouale [0000-0001-5456-8230], Rundén-Pran, Elise [0000-0002-5541-4513], Moschini, Elisa [0000-0001-9825-6263], Serchi, Tommaso [0000-0003-2386-3514], Vrček, Ivana Vinković [0000-0003-1382-5581], Burgum, Michael J. [0000-0002-3123-8914], Doak, Shareen H. [0000-0002-6753-1987], Cimpan, Mihaela Roxana [0000-0003-2029-3173], Battistelli, Chiara [0000-0003-2386-0727], Bossa, Cecilia [0000-0003-2084-2902], Tsekovska, Rositsa [0000-0001-5431-5743], Drobne, Damjana [0000-0002-5970-7460], Novak, Sara [0000-0003-0026-456X], Repar, Neža [0000-0003-4310-0362], Ammar, Ammar [0000-0002-8399-8990], Nymark, Penny [0000-0002-3435-7775], Di Battista, Veronica [0000-0002-6491-9185], Sosnowska, Anita [0000-0003-3288-4309], Puzyn, Tomasz [0000-0003-0449-8339], Kochev, Nikolay [0000-0001-6547-3675], Iliev, Luchesar [0000-0001-7000-8890], Jeliazkov, Vedrin [0000-0002-1520-5995], Reilly, Katie [0000-0002-6054-0645], Lynch, Iseult [0000-0003-4250-4584], Bakker, Martine [0000-0001-8379-7016], Delpivo, Camila [0000-0002-4413-7602], Sánchez-Jiménez, A. [0000-0002-2625-9155], Fonseca, Ana Sofia [0000-0002-1424-6365], Manier, Nicolas [0000-0003-3873-6657], Fernández-Cruz, M. L. [0000-0001-5988-1939], Rashid, Shahzad [0009-0002-3525-6607], Willighagen, Egon L. [0000-0001-7542-0286], Apostolova, Margarita D. [0000-0001-7188-506X], Dusinska, Maria [0000-0003-1358-1652], Jeliazkova, Nina, Longhin, Eleonora, El Yamani, Naouale, Rundén-Pran, Elise, Moschini, Elisa, Serchi, Tommaso, Vrček, Ivana Vinković, Burgum, Michael J., Doak, Shareen H., Cimpan, Mihaela Roxana, Rios-Mondragon, Ivan, Cimpan, Emil, Battistelli, Chiara, Bossa, Cecilia, Tsekovska, Rositsa, Drobne, Damjana, Novak, Sara, Repar, Neža, Ammar, Ammar, Nymark, Penny, Di Battista, Veronica, Sosnowska, Anita, Puzyn, Tomasz, Kochev, Nikolay, Iliev, Luchesar, Jeliazkov, Vedrin, Reilly, Katie, Lynch, Iseult, Bakker, Martine, Delpivo, Camila, Sánchez-Jiménez, A., Fonseca, Ana Sofia, Manier, Nicolas, Fernández-Cruz, M. L., Rashid, Shahzad, Willighagen, Egon L., Apostolova, Margarita D., and Dusinska, Maria

Abstract

Making research data findable, accessible, interoperable and reusable (FAIR) is typically hampered by a lack of skills in technical aspects of data management by data generators and a lack of resources. We developed a Template Wizard for researchers to easily create templates suitable for consistently capturing data and metadata from their experiments. The templates are easy to use and enable the compilation of machine-readable metadata to accompany data generation and align them to existing community standards and databases, such as eNanoMapper, streamlining the adoption of the FAIR principles. These templates are citable objects and are available as online tools. The Template Wizard is designed to be user friendly and facilitates using and reusing existing templates for new projects or project extensions. The wizard is accompanied by an online template validator, which allows self-evaluation of the template (to ensure mapping to the data schema and machine readability of the captured data) and transformation by an open-source parser into machine-readable formats, compliant with the FAIR principles. The templates are based on extensive collective experience in nanosafety data collection and include over 60 harmonized data entry templates for physicochemical characterization and hazard assessment (cell viability, genotoxicity, environmental organism dose-response tests, omics), as well as exposure and release studies. The templates are generalizable across fields and have already been extended and adapted for microplastics and advanced materials research. The harmonized templates improve the reliability of interlaboratory comparisons, data reuse and meta-analyses and can facilitate the safety evaluation and regulation process for (nano) materials.

Published
2024

7. 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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10. Drug-target identification in COVID-19 disease mechanisms using computational systems biology approaches

Author

Niarakis, Anna, Ostaszewski, Marek, Mazein, Alexander, Kuperstein, Inna, Kutmon, Martina, Gillespie, Marc E., Funahashi, Akira, Acencio, Marcio Luis, Hemedan, Ahmed, Aichem, Michael, Klein, Karsten, Czauderna, Tobias, Burtscher, Felicia, Yamada, Takahiro G., Hiki, Yusuke, Hiroi, Noriko F., Hu, Finterly, Pham, Nhung, Ehrhart, Friederike, Willighagen, Egon L., Valdeolivas, Alberto, Dugourd, Aurelien, Messina, Francesco, Esteban-Medina, Marina, Peña-Chilet, Maria, Rian, Kinza, Soliman, Sylvain, Aghamiri, Sara Sadat, Puniya, Bhanwar Lal, Naldi, Aurélien, Helikar, Tomáš, Singh, Vidisha, Fernández, Marco Fariñas, Bermudez, Viviam, Tsirvouli, Eirini, Montagud, Arnau, Noël, Vincent, Ponce-de-Leon, Miguel, Maier, Dieter, Bauch, Angela, Gyori, Benjamin M., Bachman, John A., Luna, Augustin, Piñero, Janet, Furlong, Laura I., Balaur, Irina, Rougny, Adrien, Jarosz, Yohan, Overall, Rupert, Phair, Robert, Perfetto, Livia, Matthews, Lisa, Rex, Devasahayam Arokia Balaya, Orlic-Milacic, Marija, Gomez, Luis Cristobal Monraz, De Meulder, Bertrand, Ravel, Jean Marie, Jassal, Bijay, Satagopam, Venkata, Wu, Guanming, Golebiewski, Martin, Gawron, Piotr, Calzone, Laurence, Beckmann, Jacques S., Evelo, Chris T., D’Eustachio, Peter, Schreiber, Falk, Saez-Rodriguez, Julio, Dopazo, Joaquin, Kuiper, Martin, Valencia, Alfonso, Wolkenhauer, Olaf, Kitano, Hiroaki, Barillot, Emmanuel, Auffray, Charles, Balling, Rudi, Schneider, Reinhard, Niarakis, Anna, Ostaszewski, Marek, Mazein, Alexander, Kuperstein, Inna, Kutmon, Martina, Gillespie, Marc E., Funahashi, Akira, Acencio, Marcio Luis, Hemedan, Ahmed, Aichem, Michael, Klein, Karsten, Czauderna, Tobias, Burtscher, Felicia, Yamada, Takahiro G., Hiki, Yusuke, Hiroi, Noriko F., Hu, Finterly, Pham, Nhung, Ehrhart, Friederike, Willighagen, Egon L., Valdeolivas, Alberto, Dugourd, Aurelien, Messina, Francesco, Esteban-Medina, Marina, Peña-Chilet, Maria, Rian, Kinza, Soliman, Sylvain, Aghamiri, Sara Sadat, Puniya, Bhanwar Lal, Naldi, Aurélien, Helikar, Tomáš, Singh, Vidisha, Fernández, Marco Fariñas, Bermudez, Viviam, Tsirvouli, Eirini, Montagud, Arnau, Noël, Vincent, Ponce-de-Leon, Miguel, Maier, Dieter, Bauch, Angela, Gyori, Benjamin M., Bachman, John A., Luna, Augustin, Piñero, Janet, Furlong, Laura I., Balaur, Irina, Rougny, Adrien, Jarosz, Yohan, Overall, Rupert, Phair, Robert, Perfetto, Livia, Matthews, Lisa, Rex, Devasahayam Arokia Balaya, Orlic-Milacic, Marija, Gomez, Luis Cristobal Monraz, De Meulder, Bertrand, Ravel, Jean Marie, Jassal, Bijay, Satagopam, Venkata, Wu, Guanming, Golebiewski, Martin, Gawron, Piotr, Calzone, Laurence, Beckmann, Jacques S., Evelo, Chris T., D’Eustachio, Peter, Schreiber, Falk, Saez-Rodriguez, Julio, Dopazo, Joaquin, Kuiper, Martin, Valencia, Alfonso, Wolkenhauer, Olaf, Kitano, Hiroaki, Barillot, Emmanuel, Auffray, Charles, Balling, Rudi, and Schneider, Reinhard

Abstract

Introduction: The COVID-19 Disease Map project is a large-scale community effort uniting 277 scientists from 130 Institutions around the globe. We use high-quality, mechanistic content describing SARS-CoV-2-host interactions and develop interoperable bioinformatic pipelines for novel target identification and drug repurposing. Methods: Extensive community work allowed an impressive step forward in building interfaces between Systems Biology tools and platforms. Our framework can link biomolecules from omics data analysis and computational modelling to dysregulated pathways in a cell-, tissue- or patient-specific manner. Drug repurposing using text mining and AI-assisted analysis identified potential drugs, chemicals and microRNAs that could target the identified key factors. Results: Results revealed drugs already tested for anti-COVID-19 efficacy, providing a mechanistic context for their mode of action, and drugs already in clinical trials for treating other diseases, never tested against COVID-19. Discussion: The key advance is that the proposed framework is versatile and expandable, offering a significant upgrade in the arsenal for virus-host interactions and other complex pathologies., Peer Reviewed

Published
2024

11. Building Expertise on FAIR Through Evolving Bring Your Own Data (BYOD) Workshops: Describing the Data, Software, and Management-focused Approaches and Their Evolution

Author

CMM, CMM Groep Cuppen, Bernabé, César H., Thielemans, Lieze, Kaliyaperumal, Rajaram, Carta, Claudio, Zhang, Shuxin, van Gelder, Celia W.G., Benis, Nirupama, Santos, Luiz Olavo Bonino da Silva, Cornet, Ronald, Vieira, Bruna Dos Santos, Lalout, Nawel, Henriques, Ines, Ballesteros, Alberto Cámara, Burger, Kees, Kersloot, Martijn G., Ehrhart, Friederike, Enckevort, Esther van, Evelo, Chris T., Gray, Alasdair J.G., Hanauer, Marc, Hettne, Kristina, Ligt, Joep de, Pereira, Arnaldo, Queralt-Rosinach, Núria, Schultes, Erik, Taruscio, Domenica, Waagmeester, Andra, Wilkinson, Mark D., Willighagen, Egon L., Jansen, Mascha, Mons, Barend, Roos, Marco, Jacobsen, Annika, CMM, CMM Groep Cuppen, Bernabé, César H., Thielemans, Lieze, Kaliyaperumal, Rajaram, Carta, Claudio, Zhang, Shuxin, van Gelder, Celia W.G., Benis, Nirupama, Santos, Luiz Olavo Bonino da Silva, Cornet, Ronald, Vieira, Bruna Dos Santos, Lalout, Nawel, Henriques, Ines, Ballesteros, Alberto Cámara, Burger, Kees, Kersloot, Martijn G., Ehrhart, Friederike, Enckevort, Esther van, Evelo, Chris T., Gray, Alasdair J.G., Hanauer, Marc, Hettne, Kristina, Ligt, Joep de, Pereira, Arnaldo, Queralt-Rosinach, Núria, Schultes, Erik, Taruscio, Domenica, Waagmeester, Andra, Wilkinson, Mark D., Willighagen, Egon L., Jansen, Mascha, Mons, Barend, Roos, Marco, and Jacobsen, Annika

Published
2024

12. Artificial intelligence for natural product drug discovery

Author

Mullowney, Michael W., Duncan, Katherine R., Elsayed, Somayah S., Garg, Neha, van der Hooft, Justin J. J., Martin, Nathaniel I., Meijer, David, Terlouw, Barbara R., Biermann, Friederike, Blin, Kai, Durairaj, Janani, Gonzalez, Marina Gorostiola, Helfrich, Eric J. N., Huber, Florian, Leopold-Messer, Stefan, Rajan, Kohulan, de Rond, Tristan, van Santen, Jeffrey A., Sorokina, Maria, Balunas, Marcy J., Beniddir, Mehdi A., van Bergeijk, Doris A., Carroll, Laura M., Clark, Chase M., Clevert, Djork-Arne, Dejong, Chris A., Du, Chao, Ferrinho, Scarlet, Grisoni, Francesca, Hofstetter, Albert, Jespers, Willem, Kalinina, Olga V., Kautsar, Satria A., Kim, Hyunwoo, Leao, Tiago F., Masschelein, Joleen, Rees, Evan R., Reher, Raphael, Reker, Daniel, Schwaller, Philippe, Segler, Marwin, Skinnider, Michael A., Walker, Allison S., Willighagen, Egon L., Zdrazil, Barbara, Ziemert, Nadine, Goss, Rebecca J. M., Guyomard, Pierre, Volkamer, Andrea, Gerwick, William H., Kim, Hyun Uk, Mueller, Rolf, van Wezel, Gilles P., van Westen, Gerard J. P., Hirsch, Anna K. H., Linington, Roger G., Robinson, Serina L., Medema, Marnix H., Mullowney, Michael W., Duncan, Katherine R., Elsayed, Somayah S., Garg, Neha, van der Hooft, Justin J. J., Martin, Nathaniel I., Meijer, David, Terlouw, Barbara R., Biermann, Friederike, Blin, Kai, Durairaj, Janani, Gonzalez, Marina Gorostiola, Helfrich, Eric J. N., Huber, Florian, Leopold-Messer, Stefan, Rajan, Kohulan, de Rond, Tristan, van Santen, Jeffrey A., Sorokina, Maria, Balunas, Marcy J., Beniddir, Mehdi A., van Bergeijk, Doris A., Carroll, Laura M., Clark, Chase M., Clevert, Djork-Arne, Dejong, Chris A., Du, Chao, Ferrinho, Scarlet, Grisoni, Francesca, Hofstetter, Albert, Jespers, Willem, Kalinina, Olga V., Kautsar, Satria A., Kim, Hyunwoo, Leao, Tiago F., Masschelein, Joleen, Rees, Evan R., Reher, Raphael, Reker, Daniel, Schwaller, Philippe, Segler, Marwin, Skinnider, Michael A., Walker, Allison S., Willighagen, Egon L., Zdrazil, Barbara, Ziemert, Nadine, Goss, Rebecca J. M., Guyomard, Pierre, Volkamer, Andrea, Gerwick, William H., Kim, Hyun Uk, Mueller, Rolf, van Wezel, Gilles P., van Westen, Gerard J. P., Hirsch, Anna K. H., Linington, Roger G., Robinson, Serina L., and Medema, Marnix H.

Abstract

Developments in computational omics technologies have provided new means to access the hidden diversity of natural products, unearthing new potential for drug discovery. In parallel, artificial intelligence approaches such as machine learning have led to exciting developments in the computational drug design field, facilitating biological activity prediction and de novo drug design for molecular targets of interest. Here, we describe current and future synergies between these developments to effectively identify drug candidates from the plethora of molecules produced by nature. We also discuss how to address key challenges in realizing the potential of these synergies, such as the need for high-quality datasets to train deep learning algorithms and appropriate strategies for algorithm validation.|Advances in computational omics technologies are enabling access to the hidden diversity of natural products, and artificial intelligence approaches are facilitating key steps in harnessing the therapeutic potential of such compounds, including biological activity prediction. This article discusses synergies between these fields to effectively identify drug candidates from the plethora of molecules produced by nature, and how to address the challenges in realizing the potential of these synergies.

Published
2024
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13. Erratum To: COVID‐19 Disease Map, a computational knowledge repository of virus‐host interaction mechanisms

Author

Ostaszewski, Marek, Niarakis, Anna, Mazein, Alexander, Kuperstein, Inna, Phair, Robert, Orta‐Resendiz, Aurelio, Singh, Vidisha, Aghamiri, Sara Sadat, Acencio, Marcio Luis, Glaab, Enrico, Ruepp, Andreas, Fobo, Gisela, Montrone, Corinna, Brauner, Barbara, Frishman, Goar, Monraz Gómez, Luis Cristóbal, Somers, Julia, Hoch, Matti, Kumar Gupta, Shailendra, Scheel, Julia, Borlinghaus, Hanna, Czauderna, Tobias, Schreiber, Falk, Montagud, Arnau, Ponce de Leon, Miguel, Funahashi, Akira, Hiki, Yusuke, Hiroi, Noriko, Yamada, Takahiro G, Dräger, Andreas, Renz, Alina, Naveez, Muhammad, Bocskei, Zsolt, Messina, Francesco, Börnigen, Daniela, Fergusson, Liam, Conti, Marta, Rameil, Marius, Nakonecnij, Vanessa, Vanhoefer, Jakob, Schmiester, Leonard, Wang, Muying, Ackerman, Emily E, Shoemaker, Jason E, Zucker, Jeremy, Oxford, Kristie, Teuton, Jeremy, Kocakaya, Ebru, Summak, Gökçe Yağmur, Hanspers, Kristina, Kutmon, Martina, Coort, Susan, Eijssen, Lars, Ehrhart, Friederike, Rex, D A B, Slenter, Denise, Martens, Marvin, Pham, Nhung, Haw, Robin, Jassal, Bijay, Matthews, Lisa, Orlic‐Milacic, Marija, Senff‐Ribeiro, Andrea, Rothfels, Karen, Shamovsky, Veronica, Stephan, Ralf, Sevilla, Cristoffer, Varusai, Thawfeek, Ravel, Jean‐Marie, Fraser, Rupsha, Ortseifen, Vera, Marchesi, Silvia, Gawron, Piotr, Smula, Ewa, Heirendt, Laurent, Satagopam, Venkata, Wu, Guanming, Riutta, Anders, Golebiewski, Martin, Owen, Stuart, Goble, Carole, Hu, Xiaoming, Overall, Rupert W, Maier, Dieter, Bauch, Angela, Gyori, Benjamin M, Bachman, John A, Vega, Carlos, Grouès, Valentin, Vazquez, Miguel, Porras, Pablo, Licata, Luana, Iannuccelli, Marta, Sacco, Francesca, Nesterova, Anastasia, Yuryev, Anton, de Waard, Anita, Turei, Denes, Luna, Augustin, Babur, Ozgun, Soliman, Sylvain, Valdeolivas, Alberto, Esteban‐Medina, Marina, Peña‐Chilet, Maria, Rian, Kinza, Helikar, Tomáš, Puniya, Bhanwar Lal, Modos, Dezso, Treveil, Agatha, Olbei, Marton, De Meulder, Bertrand, Ballereau, Stephane, Dugourd, Aurélien, Naldi, Aurélien, Noël, Vincent, Calzone, Laurence, Sander, Chris, Demir, Emek, Korcsmaros, Tamas, Freeman, Tom C, Augé, Franck, Beckmann, Jacques S, Hasenauer, Jan, Wolkenhauer, Olaf, Willighagen, Egon L, Pico, Alexander R, Evelo, Chris T, Gillespie, Marc E, Stein, Lincoln D, Hermjakob, Henning, D'Eustachio, Peter, Saez‐Rodriguez, Julio, Dopazo, Joaquin, Valencia, Alfonso, Kitano, Hiroaki, Barillot, Emmanuel, Auffray, Charles, Balling, Rudi, and Schneider, Reinhard

Published
2021
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17. COVID19 Disease Map, a computational knowledge repository of virus–host interaction mechanisms

Author

Ostaszewski, Marek, Niarakis, Anna, Mazein, Alexander, Kuperstein, Inna, Phair, Robert, Orta‐Resendiz, Aurelio, Singh, Vidisha, Aghamiri, Sara Sadat, Acencio, Marcio Luis, Glaab, Enrico, Ruepp, Andreas, Fobo, Gisela, Montrone, Corinna, Brauner, Barbara, Frishman, Goar, Monraz Gómez, Luis Cristóbal, Somers, Julia, Hoch, Matti, Kumar Gupta, Shailendra, Scheel, Julia, Borlinghaus, Hanna, Czauderna, Tobias, Schreiber, Falk, Montagud, Arnau, Ponce de Leon, Miguel, Funahashi, Akira, Hiki, Yusuke, Hiroi, Noriko, Yamada, Takahiro G, Dräger, Andreas, Renz, Alina, Naveez, Muhammad, Bocskei, Zsolt, Messina, Francesco, Börnigen, Daniela, Fergusson, Liam, Conti, Marta, Rameil, Marius, Nakonecnij, Vanessa, Vanhoefer, Jakob, Schmiester, Leonard, Wang, Muying, Ackerman, Emily E, Shoemaker, Jason E, Zucker, Jeremy, Oxford, Kristie, Teuton, Jeremy, Kocakaya, Ebru, Summak, Gökçe Yağmur, Hanspers, Kristina, Kutmon, Martina, Coort, Susan, Eijssen, Lars, Ehrhart, Friederike, Rex, Devasahayam Arokia Balaya, Slenter, Denise, Martens, Marvin, Pham, Nhung, Haw, Robin, Jassal, Bijay, Matthews, Lisa, Orlic‐Milacic, Marija, Senff-Ribeiro, Andrea, Rothfels, Karen, Shamovsky, Veronica, Stephan, Ralf, Sevilla, Cristoffer, Varusai, Thawfeek, Ravel, Jean‐Marie, Fraser, Rupsha, Ortseifen, Vera, Marchesi, Silvia, Gawron, Piotr, Smula, Ewa, Heirendt, Laurent, Satagopam, Venkata, Wu, Guanming, Riutta, Anders, Golebiewski, Martin, Owen, Stuart, Goble, Carole, Hu, Xiaoming, Overall, Rupert W, Maier, Dieter, Bauch, Angela, Gyori, Benjamin M, Bachman, John A, Vega, Carlos, Grouès, Valentin, Vazquez, Miguel, Porras, Pablo, Licata, Luana, Iannuccelli, Marta, Sacco, Francesca, Nesterova, Anastasia, Yuryev, Anton, de Waard, Anita, Turei, Denes, Luna, Augustin, Babur, Ozgun, Soliman, Sylvain, Valdeolivas, Alberto, Esteban‐Medina, Marina, Peña‐Chilet, Maria, Rian, Kinza, Helikar, Tomáš, Puniya, Bhanwar Lal, Modos, Dezso, Treveil, Agatha, Olbei, Marton, De Meulder, Bertrand, Ballereau, Stephane, Dugourd, Aurélien, Naldi, Aurélien, Noël, Vincent, Calzone, Laurence, Sander, Chris, Demir, Emek, Korcsmaros, Tamas, Freeman, Tom C, Augé, Franck, Beckmann, Jacques S, Hasenauer, Jan, Wolkenhauer, Olaf, Willighagen, Egon L, Pico, Alexander R, Evelo, Chris T, Gillespie, Marc E, Stein, Lincoln D, Hermjakob, Henning, D'Eustachio, Peter, Saez‐Rodriguez, Julio, Dopazo, Joaquin, Valencia, Alfonso, Kitano, Hiroaki, Barillot, Emmanuel, Auffray, Charles, Balling, Rudi, and Schneider, Reinhard

Published
2021
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18. Building expertise on FAIR through evolving Bring Your Own Data (BYOD) workshops: describing the data, software, and management- focused approaches and their evolution

Author

Bernabé, César H., primary, Thielemans, Lieze, additional, Kaliyaperumal, Rajaram, additional, Carta, Claudio, additional, Zhang, Shuxin, additional, van Gelder, Celia W.G., additional, Benis, Nirupama, additional, da Silva Santos, Luiz Olavo Bonino, additional, Cornet, Ronald, additional, Vieira, Bruna dos Santos, additional, Lalout, Nawel, additional, Henriques, Ines, additional, Ballesteros, Alberto Cámara, additional, Burger, Kees, additional, Kersloot, Martijn G., additional, Ehrhart, Friederike, additional, van Enckevort, Esther, additional, Evelo, Chris T., additional, Gray, Alasdair J. G., additional, Hanauer, Marc, additional, Hettne, Kristina, additional, de Ligt, Joep, additional, Pereira, Arnaldo, additional, Queralt-Rosinach, Núria, additional, Schultes, Erik, additional, Taruscio, Domenica, additional, Waagmeester, Andra, additional, Wilkinson, Mark D., additional, Willighagen, Egon L., additional, Jansen, Mascha, additional, Mons, Barend, additional, Roos, Marco, additional, and Jacobsen, Annika, additional

Published
2023
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19. WikiPathways 2024: next generation pathway database

Author

Agrawal, Ayushi, primary, Balcı, Hasan, additional, Hanspers, Kristina, additional, Coort, Susan L, additional, Martens, Marvin, additional, Slenter, Denise N, additional, Ehrhart, Friederike, additional, Digles, Daniela, additional, Waagmeester, Andra, additional, Wassink, Isabel, additional, Abbassi-Daloii, Tooba, additional, Lopes, Elisson N, additional, Iyer, Aishwarya, additional, Acosta, Javier Millán, additional, Willighagen, Lars G, additional, Nishida, Kozo, additional, Riutta, Anders, additional, Basaric, Helena, additional, Evelo, Chris T, additional, Willighagen, Egon L, additional, Kutmon, Martina, additional, and Pico, Alexander R, additional

Published
2023
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20. 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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22. Author Correction: COVID-19 Disease Map, building a computational repository of SARS-CoV-2 virus-host interaction mechanisms

Author

Ostaszewski, Marek, Mazein, Alexander, Gillespie, Marc E., Kuperstein, Inna, Niarakis, Anna, Hermjakob, Henning, Pico, Alexander R., Willighagen, Egon L., Evelo, Chris T., Hasenauer, Jan, Schreiber, Falk, Dräger, Andreas, Demir, Emek, Wolkenhauer, Olaf, Furlong, Laura I., Barillot, Emmanuel, Dopazo, Joaquin, Orta-Resendiz, Aurelio, Messina, Francesco, Valencia, Alfonso, Funahashi, Akira, Kitano, Hiroaki, Auffray, Charles, Balling, Rudi, and Schneider, Reinhard

Published
2020
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23. COVID-19 Disease Map, building a computational repository of SARS-CoV-2 virus-host interaction mechanisms

Author

Ostaszewski, Marek, Mazein, Alexander, Gillespie, Marc E., Kuperstein, Inna, Niarakis, Anna, Hermjakob, Henning, Pico, Alexander R., Willighagen, Egon L., Evelo, Chris T., Hasenauer, Jan, Schreiber, Falk, Dräger, Andreas, Demir, Emek, Wolkenhauer, Olaf, Furlong, Laura I., Barillot, Emmanuel, Dopazo, Joaquin, Orta-Resendiz, Aurelio, Messina, Francesco, Valencia, Alfonso, Funahashi, Akira, Kitano, Hiroaki, Auffray, Charles, Balling, Rudi, and Schneider, Reinhard

Published
2020
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24. WikiPathways 2024: next generation pathway database.

Author

Agrawal, Ayushi, Balcı, Hasan, Hanspers, Kristina, Coort, Susan L, Martens, Marvin, Slenter, Denise N, Ehrhart, Friederike, Digles, Daniela, Waagmeester, Andra, Wassink, Isabel, Abbassi-Daloii, Tooba, Lopes, Elisson N, Iyer, Aishwarya, Acosta, Javier Millán, Willighagen, Lars G, Nishida, Kozo, Riutta, Anders, Basaric, Helena, Evelo, Chris T, and Willighagen, Egon L

Published
2024
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25. Linking Nanomaterial-Induced Mitochondrial Dysfunction to Existing Adverse Outcome Pathways for Chemicals.

Author

Murugadoss, Sivakumar, Vrček, Ivana Vinković, Schaffert, Alexandra, Paparella, Martin, Pem, Barbara, Sosnowska, Anita, Stępnik, Maciej, Martens, Marvin, Willighagen, Egon L., Puzyn, Tomasz, Cimpan, Mihaela Roxana, Lemaire, Frauke, Mertens, Birgit, Dusinska, Maria, Fessard, Valérie, and Hoet, Peter H.

Abstract

The adverse outcome pathway (AOP) framework plays a crucial role in the paradigm shift of toxicity testing towards the development and use of new approach methodologies. AOPs developed for chemicals are in theory applicable to nanomaterials (NMs). However, only initial efforts have been made to integrate information on NM-induced toxicity into existing AOPs. In a previous study, we identified AOPs in the AOP-Wiki associated with the molecular initiating events (MIEs) and key events (KEs) reported for NMs in scientific literature. In a next step, we analyzed these AOPs and found that mitochondrial toxicity plays a significant role in several of them at the molecular and cellular levels. In this study, we aimed to generate hypothesis-based AOPs related to NM-induced mitochondrial toxicity. This was achieved by integrating knowledge on NM-induced mitochondrial toxicity into all existing AOPs in the AOP-Wiki, which already includes mitochondrial toxicity as a MIE/KE. Several AOPs in the AOP-Wiki related to the lung, liver, cardiovascular and nervous system, with extensively defined KEs and key event relationships (KERs), could be utilized to develop AOPs that are relevant for NMs. However, the majority of the studies included in our literature review were of poor quality, particularly in reporting NM physicochemical characteristics, and NM-relevant mitochondrial MIEs were rarely reported. This study highlights the potential role of NM-induced mitochondrial toxicity in human-relevant adverse outcomes and identifies useful AOPs in the AOP-Wiki for the development of AOPs for NMs. Plain language summary This article investigates commonalities in the toxicity pathways of chemicals and nanomaterials. Nanomaterials have been found to affect the function of mitochondria, the powerhouses within every human cell. Mitochondrial dysfunction may cause harmful effects such as cellular damage and inflammation. By linking these findings to existing adverse outcome pathways for chemicals, the research provides valuable insights for assessing the risks associated with nanomaterial exposure. This work is crucial for understanding the potential health implications of nanomaterials and can contribute to informed decision-making in regulatory and risk assessment processes without the use of animals. [ABSTRACT FROM AUTHOR]

Published
2024
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29. Drug-target identification in COVID-19 disease mechanisms using computational systems biology approaches

Author

Sanofi, Instituto de Salud Carlos III, Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), German Research Foundation, Ministero della Salute, European Commission, Generalitat de Catalunya, National Institutes of Health (US), Klaus Tschira Foundation, National Library of Medicine (US), Niarakis, Anna, Ostaszewski, Marek, Mazein, Alexander, Kuperstein, Inna, Kutmon, Martina, Gillespie, Marc E., Funahashi, Akira, Acencio, Marcio Luis, Hemedan, Ahmed, Aichem, Michael, Klein, Karsten, Czauderna, Tobias, Burtscher, Felicia, Yamada, Takahiro G., Hiki, Yusuke, Hiroi, Noriko F., Hu, Finterly, Pham, Nhung, Ehrhart, Friederike, Willighagen, Egon L., Valdeolivas, Alberto, Dugourd, Aurelien, Messina, Francesco, Esteban-Medina, Marina, Peña-Chilet, María, Rian, Kinza, Soliman, Sylvain, Aghamiri, Sara Sadat, Lal Puniya, Bhanwar, Naldi, Aurelien, Helikar, Tomas, Singh, Vidisha, Fariñas Fernández, Marco, Bermudez, Viviam, Tsirvouli, Eirini, Montagud, Arnau, Noël, Vincent, Ponce de León, Miguel, Maier, Dieter, Bauch, Angela, Gyori, Benjamin M., Bachman, John A., Luna, Augustin, Piñero, Janet, Furlong, Laura I., Balaur, Irina BalaurIrina, Rougny, Adrien, Jarosz, Yohan, Overall, Rupert W., Phair, Robert, Perfetto, Livia, Matthews, Lisa, Balaya Rex, Devasahayam Arokia, Orlic-Milacic, Marija, Monraz Gómez, Luis Cristóbal, De Meulder, Bertrand, Ravel, Jean Marie, Jassal, Bijay, Satagopam, Venkata, Wu, Guanming, Golebiewski, Martin, Gawron, Piotr, Calzone, Laurence, Beckmann, Jacques S., Evelo, Chris T., D’Eustachio, Peter, Schreiber, Falk, Sáez-Rodríguez, Julio, Dopazo, Joaquín, Kuiper, Martin, Valencia, Alfonso, Wolkenhauer, Olaf, Kitano, Hiroaki, Barillot, Emmanuel, Auffray, Charles, Balling, Rudi, Schneider, Reinhard, COVID- Disease Map Community the COVID-19 Disease Map Community, Sanofi, Instituto de Salud Carlos III, Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), German Research Foundation, Ministero della Salute, European Commission, Generalitat de Catalunya, National Institutes of Health (US), Klaus Tschira Foundation, National Library of Medicine (US), Niarakis, Anna, Ostaszewski, Marek, Mazein, Alexander, Kuperstein, Inna, Kutmon, Martina, Gillespie, Marc E., Funahashi, Akira, Acencio, Marcio Luis, Hemedan, Ahmed, Aichem, Michael, Klein, Karsten, Czauderna, Tobias, Burtscher, Felicia, Yamada, Takahiro G., Hiki, Yusuke, Hiroi, Noriko F., Hu, Finterly, Pham, Nhung, Ehrhart, Friederike, Willighagen, Egon L., Valdeolivas, Alberto, Dugourd, Aurelien, Messina, Francesco, Esteban-Medina, Marina, Peña-Chilet, María, Rian, Kinza, Soliman, Sylvain, Aghamiri, Sara Sadat, Lal Puniya, Bhanwar, Naldi, Aurelien, Helikar, Tomas, Singh, Vidisha, Fariñas Fernández, Marco, Bermudez, Viviam, Tsirvouli, Eirini, Montagud, Arnau, Noël, Vincent, Ponce de León, Miguel, Maier, Dieter, Bauch, Angela, Gyori, Benjamin M., Bachman, John A., Luna, Augustin, Piñero, Janet, Furlong, Laura I., Balaur, Irina BalaurIrina, Rougny, Adrien, Jarosz, Yohan, Overall, Rupert W., Phair, Robert, Perfetto, Livia, Matthews, Lisa, Balaya Rex, Devasahayam Arokia, Orlic-Milacic, Marija, Monraz Gómez, Luis Cristóbal, De Meulder, Bertrand, Ravel, Jean Marie, Jassal, Bijay, Satagopam, Venkata, Wu, Guanming, Golebiewski, Martin, Gawron, Piotr, Calzone, Laurence, Beckmann, Jacques S., Evelo, Chris T., D’Eustachio, Peter, Schreiber, Falk, Sáez-Rodríguez, Julio, Dopazo, Joaquín, Kuiper, Martin, Valencia, Alfonso, Wolkenhauer, Olaf, Kitano, Hiroaki, Barillot, Emmanuel, Auffray, Charles, Balling, Rudi, Schneider, Reinhard, and COVID- Disease Map Community the COVID-19 Disease Map Community

Abstract

Introduction: The COVID-19 Disease Map project is a large-scale community effort uniting 277 scientists from 130 Institutions around the globe. We use high-quality, mechanistic content describing SARS-CoV-2-host interactions and develop interoperable bioinformatic pipelines for novel target identification and drug repurposing., Methods: Extensive community work allowed an impressive step forward in building interfaces between Systems Biology tools and platforms. Our framework can link biomolecules from omics data analysis and computational modelling to dysregulated pathways in a cell-, tissue- or patient-specific manner. Drug repurposing using text mining and AI-assisted analysis identified potential drugs, chemicals and microRNAs that could target the identified key factors., Results: Results revealed drugs already tested for anti-COVID-19 efficacy, providing a mechanistic context for their mode of action, and drugs already in clinical trials for treating other diseases, never tested against COVID-19., Discussion: The key advance is that the proposed framework is versatile and expandable, offering a significant upgrade in the arsenal for virus-host interactions and other complex pathologies.

Published
2023

30. Guiding the choice of informatics software and tools for lipidomics research applications

Author

Ni, Zhixu, primary, Wölk, Michele, additional, Jukes, Geoff, additional, Mendivelso Espinosa, Karla, additional, Ahrends, Robert, additional, Aimo, Lucila, additional, Alvarez-Jarreta, Jorge, additional, Andrews, Simon, additional, Andrews, Robert, additional, Bridge, Alan, additional, Clair, Geremy C., additional, Conroy, Matthew J., additional, Fahy, Eoin, additional, Gaud, Caroline, additional, Goracci, Laura, additional, Hartler, Jürgen, additional, Hoffmann, Nils, additional, Kopczyinki, Dominik, additional, Korf, Ansgar, additional, Lopez-Clavijo, Andrea F., additional, Malik, Adnan, additional, Ackerman, Jacobo Miranda, additional, Molenaar, Martijn R., additional, O’Donovan, Claire, additional, Pluskal, Tomáš, additional, Shevchenko, Andrej, additional, Slenter, Denise, additional, Siuzdak, Gary, additional, Kutmon, Martina, additional, Tsugawa, Hiroshi, additional, Willighagen, Egon L., additional, Xia, Jianguo, additional, O’Donnell, Valerie B., additional, and Fedorova, Maria, additional

Published
2022
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34. Humans of AI3SD: Egon Willighagen

Author

Pauli, Michelle, Willighagen, Egon L., Frey, Jeremy G., Kanza, Samantha, and Niranjan, Mahesan

Subjects
AI3SD, Interview
Abstract

This interview forms part of the Humans of AI3SD SeriesIn this Humans of AI3SD interview he discusses the growth of open science over the past 20 years and the continued need for it, the challenge of deep learning methods, and his advice for early career researchers.

Published
2022

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. Fair principles: Interpretations and implementation considerations

Author

European Commission, Universidad Politécnica de Madrid, Ministerio de Economía y Competitividad (España), Jacobsen, Annika [0000-0003-4818-2360], De Miranda Azevedo, Ricardo [0000-0002-7641-6446], Juty, Nick [0000-0002-2036-8350], Batista, Dominique [0000-0002-2109-489X], Coles, Simon [0000-0001-8414-9272], Cornet, Ronald [0000-0002-1704-5980], Courtot, Mélanie [0000-0002-9551-6370], Crosas, Mercè [0000-0003-1304-1939], Dumontier, Michel [0000-0003-4727-9435], Evelo, Chris T. A. [0000-0002-5301-3142], Goble, Carole [0000-0003-1219-2137], Guizzardi, Giancarlo [0000-0002-3452-553X], Hansen, Karsten [0000-0002-2407-8764], Hasnain, Ali [0000-0003-4014-4394], Hettne, Kristina [0000-0002-4182-7560], Heringa, Jaap [0000-0001-8641-4930], Hooft, Rob W.W. [0000-0001-6825-9439], Imming, Melanie [0000-0003-2376-9755], Jeffery, Keith [0000-0003-4053-7825], Kaliyaperumal, Rajaram [0000-0002-1215-167X], Kersloot, Martijn [0000-0003-3357-3027], Kirkpatrick, Christine R. [0000-0002-4451-8042], Kuhn, Tobias [0000-0002-1267-0234], Labastida, Ignasi [0000-0001-7030-7030], Magagna, Barbara [0000-0003-2195-3997], McQuilton, Peter [0000-0003-2687-1982], Meyers, Natalie [0000-0001-6441-6716], Montesanti, Annalisa [0000-0003-0413-2003], Van Reisen, Mirjam [0000-0003-0627-8014], Rocca-Serra, Philippe [0000-0001-9853-5668], Pergl, Robert [0000-0003-2980-4400], Sansone, Susanna Assunta [0000-0001-5306-5690], Santos, Luiz Olavo Bonino da Silva [0000-0002-1164-1351], Schneider, Juliane [0000-0002-7664-3331], Strawn, George [0000-0003-4098-0464], Waagmeester, Andra S. [0000-0001-9773-4008], Weigel, Tobias [0000-0002-4040-0215], Wilkinson, Mark D. [0000-0001-6960-357X], Willighagen, Egon L. [0000-0001-7542-0286], Wittenburg, Peter [0000-0003-3538-0106], Roos, Marco [0000-0002-8691-772X], Mons, Barend [0000-0003-3934-0072], Schultes, Erik [0000-0001-8888-635X], Jacobsen, Annika, De Miranda Azevedo, Ricardo, Juty, Nick, Batista, Dominique, Coles, Simon, Cornet, Ronald, Courtot, Mélanie, Crosas, Mercè, Dumontier, Michel, Evelo, Chris T. A., Goble, Carole, Guizzardi, Giancarlo, Hansen, Karsten, Hasnain, Ali, Hettne, Kristina, Heringa, Jaap, Hooft, Rob W.W., Imming, Melanie, Jeffery, Keith, Kaliyaperumal, Rajaram, Kersloot, Martijn, Kirkpatrick, Christine R., Kuhn, Tobias, Labastida, Ignasi, Magagna, Barbara, McQuilton, Peter, Meyers, Natalie, Montesanti, Annalisa, Van Reisen, Mirjam, Rocca-Serra, Philippe, Pergl, Robert, Sansone, Susanna Assunta, Santos, Luiz Olavo Bonino da Silva, Schneider, Juliane, Strawn, George, Thompson, Mark, Waagmeester, Andra S., Weigel, Tobias, Wilkinson, Mark D., Willighagen, Egon L., Wittenburg, Peter, Roos, Marco, Mons, Barend, Schultes, Erik, European Commission, Universidad Politécnica de Madrid, Ministerio de Economía y Competitividad (España), Jacobsen, Annika [0000-0003-4818-2360], De Miranda Azevedo, Ricardo [0000-0002-7641-6446], Juty, Nick [0000-0002-2036-8350], Batista, Dominique [0000-0002-2109-489X], Coles, Simon [0000-0001-8414-9272], Cornet, Ronald [0000-0002-1704-5980], Courtot, Mélanie [0000-0002-9551-6370], Crosas, Mercè [0000-0003-1304-1939], Dumontier, Michel [0000-0003-4727-9435], Evelo, Chris T. A. [0000-0002-5301-3142], Goble, Carole [0000-0003-1219-2137], Guizzardi, Giancarlo [0000-0002-3452-553X], Hansen, Karsten [0000-0002-2407-8764], Hasnain, Ali [0000-0003-4014-4394], Hettne, Kristina [0000-0002-4182-7560], Heringa, Jaap [0000-0001-8641-4930], Hooft, Rob W.W. [0000-0001-6825-9439], Imming, Melanie [0000-0003-2376-9755], Jeffery, Keith [0000-0003-4053-7825], Kaliyaperumal, Rajaram [0000-0002-1215-167X], Kersloot, Martijn [0000-0003-3357-3027], Kirkpatrick, Christine R. [0000-0002-4451-8042], Kuhn, Tobias [0000-0002-1267-0234], Labastida, Ignasi [0000-0001-7030-7030], Magagna, Barbara [0000-0003-2195-3997], McQuilton, Peter [0000-0003-2687-1982], Meyers, Natalie [0000-0001-6441-6716], Montesanti, Annalisa [0000-0003-0413-2003], Van Reisen, Mirjam [0000-0003-0627-8014], Rocca-Serra, Philippe [0000-0001-9853-5668], Pergl, Robert [0000-0003-2980-4400], Sansone, Susanna Assunta [0000-0001-5306-5690], Santos, Luiz Olavo Bonino da Silva [0000-0002-1164-1351], Schneider, Juliane [0000-0002-7664-3331], Strawn, George [0000-0003-4098-0464], Waagmeester, Andra S. [0000-0001-9773-4008], Weigel, Tobias [0000-0002-4040-0215], Wilkinson, Mark D. [0000-0001-6960-357X], Willighagen, Egon L. [0000-0001-7542-0286], Wittenburg, Peter [0000-0003-3538-0106], Roos, Marco [0000-0002-8691-772X], Mons, Barend [0000-0003-3934-0072], Schultes, Erik [0000-0001-8888-635X], Jacobsen, Annika, De Miranda Azevedo, Ricardo, Juty, Nick, Batista, Dominique, Coles, Simon, Cornet, Ronald, Courtot, Mélanie, Crosas, Mercè, Dumontier, Michel, Evelo, Chris T. A., Goble, Carole, Guizzardi, Giancarlo, Hansen, Karsten, Hasnain, Ali, Hettne, Kristina, Heringa, Jaap, Hooft, Rob W.W., Imming, Melanie, Jeffery, Keith, Kaliyaperumal, Rajaram, Kersloot, Martijn, Kirkpatrick, Christine R., Kuhn, Tobias, Labastida, Ignasi, Magagna, Barbara, McQuilton, Peter, Meyers, Natalie, Montesanti, Annalisa, Van Reisen, Mirjam, Rocca-Serra, Philippe, Pergl, Robert, Sansone, Susanna Assunta, Santos, Luiz Olavo Bonino da Silva, Schneider, Juliane, Strawn, George, Thompson, Mark, Waagmeester, Andra S., Weigel, Tobias, Wilkinson, Mark D., Willighagen, Egon L., Wittenburg, Peter, Roos, Marco, Mons, Barend, and Schultes, Erik

Abstract

The FAIR principles have been widely cited, endorsed and adopted by a broad range of stakeholders since their publication in 2016. By intention, the 15 FAIR guiding principles do not dictate specific technological implementations, but provide guidance for improving Findability, Accessibility, Interoperability and Reusability of digital resources. This has likely contributed to the broad adoption of the FAIR principles, because individual stakeholder communities can implement their own FAIR solutions. However, it has also resulted in inconsistent interpretations that carry the risk of leading to incompatible implementations. Thus, while the FAIR principles are formulated on a high level and may be interpreted and implemented in different ways, for true interoperability we need to support convergence in implementation choices that are widely accessible and (re)-usable. We introduce the concept of FAIR implementation considerations to assist accelerated global participation and convergence towards accessible, robust, widespread and consistent FAIR implementations. Any self-identified stakeholder community may either choose to reuse solutions from existing implementations, or when they spot a gap, accept the challenge to create the needed solution, which, ideally, can be used again by other communities in the future. Here, we provide interpretations and implementation considerations (choices and challenges) for each FAIR principle.

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
Full Text
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39. 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

40. 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

41. 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

44. 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
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47. Ten simple rules for creating reusable pathway models for computational analysis and visualization

Author

Hanspers, Kristina, Kutmon, Martina, Coort, Susan L., Digles, Daniela, Dupuis, Lauren J., Ehrhart, Friederike, Hu, Finterly, Lopes, Elisson N., Martens, Marvin, Pham, Nhung, Shin, Woosub, Slenter, Denise N., Waagmeester, Andra, Willighagen, Egon L., Winckers, Laurent A., Evelo, Chris T., Pico, Alexander R., Bioinformatica, RS: FSE MaCSBio, RS: FPN MaCSBio, RS: FHML MaCSBio, Maastricht Centre for Systems Biology, RS: NUTRIM - R1 - Obesity, diabetes and cardiovascular health, and RS: NUTRIM - R3 - Respiratory & Age-related Health

Subjects
Metabolic Processes, Databases, Factual, Computer science, Semantics (computer science), Social Sciences, computer.software_genre, Biochemistry, Simple (abstract algebra), Medicine and Health Sciences, Drug Interactions, Computational analysis, Biology (General), Data Management, Protein Metabolism, Ecology, Programming language, Semantics, Editorial, Computational Theory and Mathematics, Modeling and Simulation, Metabolic Pathways, Metabolic Networks and Pathways, Computer and Information Sciences, DATABASE, QH301-705.5, Models, Biological, Cellular and Molecular Neuroscience, Data visualization, RESOURCE, Terminology as Topic, Citric acid cycle, Genetics, Ontologies, Computer Graphics, Animals, Humans, KNOWLEDGE, Protein Interactions, Molecular Biology, Ecology, Evolution, Behavior and Systematics, Pharmacology, business.industry, Data Visualization, PLATFORM, Biology and Life Sciences, Proteins, Computational Biology, Linguistics, GENE, Database searching, Visualization, Metabolism, business, computer
Abstract

The abstract is available here: https://uscholar.univie.ac.at/o:1603275

Published
2021

48. 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
2021
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50. WikiPathways: connecting communities

Author

Martens, Marvin, Ammar, Ammar, Riutta, Anders, Waagmeester, Andra, Slenter, Denise N, Hanspers, Kristina, A. Miller, Ryan, Digles, Daniela, Lopes, Elisson N, Ehrhart, Friederike, Dupuis, Lauren J, Winckers, Laurent A, Coort, Susan L, Willighagen, Egon L, Evelo, Chris T, Pico, Alexander R, Kutmon, Martina, Bioinformatica, RS: NUTRIM - R1 - Obesity, diabetes and cardiovascular health, RS: NUTRIM - R3 - Respiratory & Age-related Health, RS: FHML MaCSBio, Maastricht Centre for Systems Biology, RS: FSE MaCSBio, and RS: FPN MaCSBio

Subjects
0303 health sciences, Open science, 2019-20 coronavirus outbreak, Databases, Factual, Coronavirus disease 2019 (COVID-19), AcademicSubjects/SCI00010, WikiPathways : Pathways for the people, Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), Pathway database, Publications, SET ENRICHMENT ANALYSIS, COVID-19, Biology, FRAMEWORK, World Wide Web, User-Computer Interface, 03 medical and health sciences, 0302 clinical medicine, Genetics, Humans, Database Issue, Data Curation, 030217 neurology & neurosurgery, 030304 developmental biology
Abstract

WikiPathways (https://www.wikipathways.org) is a biological pathway database known for its collaborative nature and open science approaches. With the core idea of the scientific community developing and curating biological knowledge in pathway models, WikiPathways lowers all barriers for accessing and using its content. Increasingly more content creators, initiatives, projects and tools have started using WikiPathways. Central in this growth and increased use of WikiPathways are the various communities that focus on particular subsets of molecular pathways such as for rare diseases and lipid metabolism. Knowledge from published pathway figures helps prioritize pathway development, using optical character and named entity recognition. We show the growth of WikiPathways over the last three years, highlight the new communities and collaborations of pathway authors and curators, and describe various technologies to connect to external resources and initiatives. The road toward a sustainable, community-driven pathway database goes through integration with other resources such as Wikidata and allowing more use, curation and redistribution of WikiPathways content., Graphical Abstract Graphical AbstractWikiPathways enables research communities to collaborate on molecular pathway curation to create reusable, machine-readable pathway models. The pathway collections are freely available and integrated with many analysis tools and resources.

Published
2021

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