Author: "Willighagen, Egon L" - Searchworks@Jio Institute Digital Library Search Results

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338 results on '"Willighagen, Egon L"'

1. From papers to RDF-based integration of physicochemical data and adverse outcome pathways for nanomaterials

Author: van Rijn, Jeaphianne P. M., Martens, Marvin, Ammar, Ammar, Cimpan, Mihaela Roxana, Fessard, Valerie, Hoet, Peter, Jeliazkova, Nina, Murugadoss, Sivakumar, Vinković Vrček, Ivana, and Willighagen, Egon L.
Published: 2024
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2. 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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3. Author Correction: A protocol for adding knowledge to Wikidata: aligning resources on human coronaviruses

Author: Waagmeester, Andra, Willighagen, Egon L., Su, Andrew I., Kutmon, Martina, Gayo, Jose Emilio Labra, Fernández-Álvarez, Daniel, Groom, Quentin, Schaap, Peter J., Verhagen, Lisa M., and Koehorst, Jasper J.
Published: 2023
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4. Extending inherited metabolic disorder diagnostics with biomarker interaction visualizations

Author: Slenter, Denise N., Hemel, Irene M. G. M., Evelo, Chris T., Bierau, Jörgen, Willighagen, Egon L., and Steinbusch, Laura K. M.
Published: 2023
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5. 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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6. 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. WikiPathways: Integrating Pathway Knowledge with Clinical Data

Author: Slenter, Denise N., Kutmon, Martina, Willighagen, Egon L., Blau, Nenad, editor, Dionisi Vici, Carlo, editor, Ferreira, Carlos R., editor, Vianey-Saban, Christine, editor, and van Karnebeek, Clara D. M., editor
Published: 2022
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8. 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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9. Research Techniques Made Simple: Lipidomic Analysis in Skin Research

Author: Sochorová, Michaela, Vávrová, Kateřina, Fedorova, Maria, Ni, Zhixu, Slenter, Denise, Kutmon, Martina, Willighagen, Egon L., Letsiou, Sophia, Töröcsik, Daniel, Marchetti-Deschmann, Martina, Zoratto, Samuele, Kremslehner, Christopher, and Gruber, Florian
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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14. A resource to explore the discovery of rare diseases and their causative genes

Author: Ehrhart, Friederike, Willighagen, Egon L., Kutmon, Martina, van Hoften, Max, Curfs, Leopold M. G., and Evelo, Chris T.
Published: 2021
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15. A catalogue of 863 Rett-syndrome-causing MECP2 mutations and lessons learned from data integration

Author: Ehrhart, Friederike, Jacobsen, Annika, Rigau, Maria, Bosio, Mattia, Kaliyaperumal, Rajaram, Laros, Jeroen F. J., Willighagen, Egon L., Valencia, Alfonso, Roos, Marco, Capella-Gutierrez, Salvador, Curfs, Leopold M. G., and Evelo, Chris T.
Published: 2021
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16. A protocol for adding knowledge to Wikidata: aligning resources on human coronaviruses

Author: Waagmeester, Andra, Willighagen, Egon L., Su, Andrew I., Kutmon, Martina, Gayo, Jose Emilio Labra, Fernández-Álvarez, Daniel, Groom, Quentin, Schaap, Peter J., Verhagen, Lisa M., and Koehorst, Jasper J.
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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21. Integration among databases and data sets to support productive nanotechnology: Challenges and recommendations

Author: Karcher, Sandra, Willighagen, Egon L., Rumble, John, Ehrhart, Friederike, Evelo, Chris T., Fritts, Martin, Gaheen, Sharon, Harper, Stacey L., Hoover, Mark D., Jeliazkova, Nina, Lewinski, Nastassja, Marchese Robinson, Richard L., Mills, Karmann C., Mustad, Axel P., Thomas, Dennis G., Tsiliki, Georgia, and Hendren, Christine Ogilvie
Published: 2018
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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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26. Discovering life’s directed metabolic (sub)paths to interpret biochemical markers using the DSMN

Author: Slenter, Denise, primary, Kutmon, M., additional, Evelo, Chris T., additional, and Willighagen, Egon L., additional
Published: 2023
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27. Molecular Adverse Outcome Pathways: towards the implementation of transcriptomics data in risk assessments

Author: Martens, Marvin, primary, Meuleman, Anna Baya, additional, Kearns, Jeroen, additional, de Windt, Chesley, additional, Evelo, Chris T., additional, and Willighagen, Egon L., additional
Published: 2023
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28. The Chemistry Development Kit (CDK) v2.0: atom typing, depiction, molecular formulas, and substructure searching

Author: Willighagen, Egon L., Mayfield, John W., Alvarsson, Jonathan, Berg, Arvid, Carlsson, Lars, Jeliazkova, Nina, Kuhn, Stefan, Pluskal, Tomáš, Rojas-Chertó, Miquel, Spjuth, Ola, Torrance, Gilleain, Evelo, Chris T., Guha, Rajarshi, and Steinbeck, Christoph
Published: 2017
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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. Scientific Lenses to Support Multiple Views over Linked Chemistry Data

Author: Batchelor, Colin, Brenninkmeijer, Christian Y. A., Chichester, Christine, Davies, Mark, Digles, Daniela, Dunlop, Ian, Evelo, Chris T., Gaulton, Anna, Goble, Carole, Gray, Alasdair J. G., Groth, Paul, Harland, Lee, Karapetyan, Karen, Loizou, Antonis, Overington, John P., Pettifer, Steve, Steele, Jon, Stevens, Robert, Tkachenko, Valery, Waagmeester, Andra, Williams, Antony, Willighagen, Egon L., Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Kobsa, Alfred, Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Nierstrasz, Oscar, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Weikum, Gerhard, Series editor, Mika, Peter, editor, Tudorache, Tania, editor, Bernstein, Abraham, editor, Welty, Chris, editor, Knoblock, Craig, editor, Vrandečić, Denny, editor, Groth, Paul, editor, Noy, Natasha, editor, Janowicz, Krzysztof, editor, and Goble, Carole, editor
Published: 2014
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31. 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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32. XMetDB: an open access database for xenobiotic metabolism

Author: Spjuth, Ola, Rydberg, Patrik, Willighagen, Egon L., Evelo, Chris T., and Jeliazkova, Nina
Published: 2016
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33. Incorporating Commercial and Private Data into an Open Linked Data Platform for Drug Discovery

Author: Goble, Carole, Gray, Alasdair J. G., Harland, Lee, Karapetyan, Karen, Loizou, Antonis, Mikhailov, Ivan, Rankka, Yrjänä, Senger, Stefan, Tkachenko, Valery, Williams, Antony J., Willighagen, Egon L., Hutchison, David, editor, Kanade, Takeo, editor, Kittler, Josef, editor, Kleinberg, Jon M., editor, Mattern, Friedemann, editor, Mitchell, John C., editor, Naor, Moni, editor, Nierstrasz, Oscar, editor, Pandu Rangan, C., editor, Steffen, Bernhard, editor, Sudan, Madhu, editor, Terzopoulos, Demetri, editor, Tygar, Doug, editor, Vardi, Moshe Y., editor, Weikum, Gerhard, editor, Alani, Harith, editor, Kagal, Lalana, editor, Fokoue, Achille, editor, Groth, Paul, editor, Biemann, Chris, editor, Parreira, Josiane Xavier, editor, Aroyo, Lora, editor, Noy, Natasha, editor, Welty, Chris, editor, and Janowicz, Krzysztof, editor
Published: 2013
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34. Wikipedia on the CompTox Chemicals Dashboard: Connecting Resources to Enrich Public Chemical Data

Author: Sinclair, Gabriel, primary, Thillainadarajah, Inthirany, additional, Meyer, Brian, additional, Samano, Vicente, additional, Sivasupramaniam, Sakuntala, additional, Adams, Linda, additional, Willighagen, Egon L., additional, Richard, Ann M., additional, Walker, Martin, additional, and Williams, Antony J., additional
Published: 2022
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35. Discovering life’s directed metabolic (sub)paths to interpret biochemical markers using the DSMN

Author: Slenter, Denise, primary, Kutmon, M., additional, Evelo, Chris T., additional, and Willighagen, Egon L., additional
Published: 2022
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36. 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

37. RRegrs: an R package for computer-aided model selection with multiple regression models

Author: Tsiliki, Georgia, Munteanu, Cristian R., Seoane, Jose A., Fernandez-Lozano, Carlos, Sarimveis, Haralambos, and Willighagen, Egon L.
Published: 2015
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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, 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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39. 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

40. 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: View/download PDF

41. 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

42. 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

43. 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. Open PHACTS: semantic interoperability for drug discovery

Author: Williams, Antony J., Harland, Lee, Groth, Paul, Pettifer, Stephen, Chichester, Christine, Willighagen, Egon L., Evelo, Chris T., Blomberg, Niklas, Ecker, Gerhard, Goble, Carole, and Mons, Barend
Published: 2012
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45. Understanding signaling and metabolic paths using semantified and harmonized information about biological interactions

Author: Miller, Ryan A., primary, Kutmon, Martina, additional, Bohler, Anwesha, additional, Waagmeester, Andra, additional, Evelo, Chris T., additional, and Willighagen, Egon L., additional
Published: 2022
Full Text: View/download PDF

46. Providing Adverse Outcome Pathways from the AOP-Wiki in a Semantic Web Format to Increase Usability and Accessibility of the Content

Author: Martens, Marvin, primary, Evelo, Chris T., additional, and Willighagen, Egon L., additional
Published: 2022
Full Text: View/download PDF

47. 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: View/download PDF

48. The AOP-DB RDF: Applying FAIR Principles to the Semantic Integration of AOP Data Using the Research Description Framework

Author: Mortensen, Holly M., primary, Martens, Marvin, additional, Senn, Jonathan, additional, Levey, Trevor, additional, Evelo, Chris T., additional, Willighagen, Egon L., additional, and Exner, Thomas, additional
Published: 2022
Full Text: View/download PDF

49. Extending Inherited Metabolic Disorder diagnostics with Biomarker Interaction Visualizations

Author: Slenter, Denise N., primary, Hemel, Irene M.G.M., additional, Evelo, Chris T., additional, Bierau, Jörgen, additional, Willighagen, Egon L., additional, and Steinbusch, Laura K.M., additional
Published: 2022
Full Text: View/download PDF

50. Applications of the InChI in cheminformatics with the CDK and Bioclipse

Author: Spjuth, Ola, Berg, Arvid, Adams, Samuel, and Willighagen, Egon L
Published: 2013
Full Text: View/download PDF

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