COVID19 Disease Map, a computational knowledge repository of virus-host interaction mechanisms

Ostaszewski M, Niarakis A, Mazein A, Kuperstein I, Phair R, Orta-Resendiz A, Singh V, Aghamiri SS, Acencio ML, Glaab E, Ruepp A, et al. (2021)
Molecular systems biology 17(10): e10387.

Zeitschriftenaufsatz | Veröffentlicht | Englisch
 
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Autor*in
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
Alle
Abstract / Bemerkung
We need to effectively combine the knowledge from surging literature with complex datasets to propose mechanistic models of SARS-CoV-2 infection, improving data interpretation and predicting key targets of intervention. Here, we describe a large-scale community effort to build an open access, interoperable and computable repository of COVID-19 molecular mechanisms. The COVID-19 Disease Map (C19DMap) is a graphical, interactive representation of disease-relevant molecular mechanisms linking many knowledge sources. Notably, it is a computational resource for graph-based analyses and disease modelling. To this end, we established a framework of tools, platforms and guidelines necessary for a multifaceted community of biocurators, domain experts, bioinformaticians and computational biologists. The diagrams of the C19DMap, curated from the literature, are integrated with relevant interaction and text mining databases. We demonstrate the application of network analysis and modelling approaches by concrete examples to highlight new testable hypotheses. This framework helps to find signatures of SARS-CoV-2 predisposition, treatment response or prioritisation of drug candidates. Such an approach may help deal with new waves of COVID-19 or similar pandemics in the long-term perspective. © 2021 The Authors. Published under the terms of the CC BY 4.0 license.
Erscheinungsjahr
2021
Zeitschriftentitel
Molecular systems biology
Band
17
Ausgabe
10
Art.-Nr.
e10387
eISSN
1744-4292
Page URI
https://pub.uni-bielefeld.de/record/2958751

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Ostaszewski M, Niarakis A, Mazein A, et al. COVID19 Disease Map, a computational knowledge repository of virus-host interaction mechanisms. Molecular systems biology. 2021;17(10): e10387.
Ostaszewski, M., Niarakis, A., Mazein, A., Kuperstein, I., Phair, R., Orta-Resendiz, A., Singh, V., et al. (2021). COVID19 Disease Map, a computational knowledge repository of virus-host interaction mechanisms. Molecular systems biology, 17(10), e10387. https://doi.org/10.15252/msb.202110387
Ostaszewski, M., Niarakis, A., Mazein, A., Kuperstein, I., Phair, R., Orta-Resendiz, A., Singh, V., Aghamiri, S. S., Acencio, M. L., Glaab, E., et al. (2021). COVID19 Disease Map, a computational knowledge repository of virus-host interaction mechanisms. Molecular systems biology 17:e10387.
Ostaszewski, M., et al., 2021. COVID19 Disease Map, a computational knowledge repository of virus-host interaction mechanisms. Molecular systems biology, 17(10): e10387.
M. Ostaszewski, et al., “COVID19 Disease Map, a computational knowledge repository of virus-host interaction mechanisms”, Molecular systems biology, vol. 17, 2021, : e10387.
Ostaszewski, M., Niarakis, A., Mazein, A., Kuperstein, I., Phair, R., Orta-Resendiz, A., Singh, V., Aghamiri, S.S., Acencio, M.L., Glaab, E., Ruepp, A., Fobo, G., Montrone, C., Brauner, B., Frishman, G., Monraz Gomez, L.C., Somers, J., Hoch, M., Kumar Gupta, S., Scheel, J., Borlinghaus, H., Czauderna, T., Schreiber, F., Montagud, A., Ponce de Leon, M., Funahashi, A., Hiki, Y., Hiroi, N., Yamada, T.G., Drager, A., Renz, A., Naveez, M., Bocskei, Z., Messina, F., Bornigen, D., Fergusson, L., Conti, M., Rameil, M., Nakonecnij, V., Vanhoefer, J., Schmiester, L., Wang, M., Ackerman, E.E., Shoemaker, J.E., Zucker, J., Oxford, K., Teuton, J., Kocakaya, E., Summak, G.Y., Hanspers, K., Kutmon, M., Coort, S., Eijssen, L., Ehrhart, F., Rex, D.A.B., Slenter, D., Martens, M., Pham, N., Haw, R., Jassal, B., Matthews, L., Orlic-Milacic, M., Senff Ribeiro, A., Rothfels, K., Shamovsky, V., Stephan, R., Sevilla, C., Varusai, T., Ravel, J.-M., Fraser, R., Ortseifen, V., Marchesi, S., Gawron, P., Smula, E., Heirendt, L., Satagopam, V., Wu, G., Riutta, A., Golebiewski, M., Owen, S., Goble, C., Hu, X., Overall, R.W., Maier, D., Bauch, A., Gyori, B.M., Bachman, J.A., Vega, C., Groues, V., Vazquez, M., Porras, P., Licata, L., Iannuccelli, M., Sacco, F., Nesterova, A., Yuryev, A., de Waard, A., Turei, D., Luna, A., Babur, O., Soliman, S., Valdeolivas, A., Esteban-Medina, M., Pena-Chilet, M., Rian, K., Helikar, T., Puniya, B.L., Modos, D., Treveil, A., Olbei, M., De Meulder, B., Ballereau, S., Dugourd, A., Naldi, A., Noel, V., Calzone, L., Sander, C., Demir, E., Korcsmaros, T., Freeman, T.C., Auge, F., Beckmann, J.S., Hasenauer, J., Wolkenhauer, O., Wilighagen, E.L., Pico, A.R., Evelo, C.T., Gillespie, M.E., Stein, L.D., Hermjakob, H., D'Eustachio, P., Saez-Rodriguez, J., Dopazo, J., Valencia, A., Kitano, H., Barillot, E., Auffray, C., Balling, R., Schneider, R.: COVID19 Disease Map, a computational knowledge repository of virus-host interaction mechanisms. Molecular systems biology. 17, : e10387 (2021).
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 Gomez, Luis Cristobal, 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, Drager, Andreas, Renz, Alina, Naveez, Muhammad, Bocskei, Zsolt, Messina, Francesco, Bornigen, 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, Gokce Yagmur, 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, Groues, 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, Pena-Chilet, Maria, Rian, Kinza, Helikar, Tomas, Puniya, Bhanwar Lal, Modos, Dezso, Treveil, Agatha, Olbei, Marton, De Meulder, Bertrand, Ballereau, Stephane, Dugourd, Aurelien, Naldi, Aurelien, Noel, Vincent, Calzone, Laurence, Sander, Chris, Demir, Emek, Korcsmaros, Tamas, Freeman, Tom C, Auge, Franck, Beckmann, Jacques S, Hasenauer, Jan, Wolkenhauer, Olaf, Wilighagen, 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. “COVID19 Disease Map, a computational knowledge repository of virus-host interaction mechanisms”. Molecular systems biology 17.10 (2021): e10387.

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