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@ARTICLE{Ostaszewski:162909,
author = {Ostaszewski, Marek and Niarakis, Anna and Mazein, Alexander
and Kuperstein, Inna and Phair, Robert and Orta-Resendiz,
Aurelio and Singh, Vidisha and Aghamiri, Sara Sadat and
Acencio, Marcio Luis and Glaab, Enrico and Ruepp, Andreas
and Fobo, Gisela and Montrone, Corinna and Brauner, Barbara
and Frishman, Goar and Monraz Gómez, Luis Cristóbal and
Somers, Julia and Hoch, Matti and Kumar Gupta, Shailendra
and Scheel, Julia and Borlinghaus, Hanna and Czauderna,
Tobias and Schreiber, Falk and Montagud, Arnau and Ponce de
Leon, Miguel and Funahashi, Akira and Hiki, Yusuke and
Hiroi, Noriko and Yamada, Takahiro G and Dräger, Andreas
and Renz, Alina and Naveez, Muhammad and Bocskei, Zsolt and
Messina, Francesco and Börnigen, Daniela and Fergusson,
Liam and Conti, Marta and Rameil, Marius and Nakonecnij,
Vanessa and Vanhoefer, Jakob and Schmiester, Leonard and
Wang, Muying and Ackerman, Emily E and Shoemaker, Jason E
and Zucker, Jeremy and Oxford, Kristie and Teuton, Jeremy
and Kocakaya, Ebru and Summak, Gökçe Yağmur and Hanspers,
Kristina and Kutmon, Martina and Coort, Susan and Eijssen,
Lars and Ehrhart, Friederike and Rex, Devasahayam Arokia
Balaya and Slenter, Denise and Martens, Marvin and Pham,
Nhung and Haw, Robin and Jassal, Bijay and Matthews, Lisa
and Orlic-Milacic, Marija and Senff Ribeiro, Andrea and
Rothfels, Karen and Shamovsky, Veronica and Stephan, Ralf
and Sevilla, Cristoffer and Varusai, Thawfeek and Ravel,
Jean-Marie and Fraser, Rupsha and Ortseifen, Vera and
Marchesi, Silvia and Gawron, Piotr and Smula, Ewa and
Heirendt, Laurent and Satagopam, Venkata and Wu, Guanming
and Riutta, Anders and Golebiewski, Martin and Owen, Stuart
and Goble, Carole and Hu, Xiaoming and Overall, Rupert and
Maier, Dieter and Bauch, Angela and Gyori, Benjamin M and
Bachman, John A and Vega, Carlos and Grouès, Valentin and
Vazquez, Miguel and Porras, Pablo and Licata, Luana and
Iannuccelli, Marta and Sacco, Francesca and Nesterova,
Anastasia and Yuryev, Anton and de Waard, Anita and Turei,
Denes and Luna, Augustin and Babur, Ozgun and Soliman,
Sylvain and Valdeolivas, Alberto and Esteban-Medina, Marina
and Peña-Chilet, Maria and Rian, Kinza and Helikar, Tomáš
and Puniya, Bhanwar Lal and Modos, Dezso and Treveil, Agatha
and Olbei, Marton and De Meulder, Bertrand and Ballereau,
Stephane and Dugourd, Aurélien and Naldi, Aurélien and
Noël, Vincent and Calzone, Laurence and Sander, Chris and
Demir, Emek and Korcsmaros, Tamas and Freeman, Tom C and
Augé, Franck and Beckmann, Jacques S and Hasenauer, Jan and
Wolkenhauer, Olaf and Wilighagen, Egon L and Pico, Alexander
R and Evelo, Chris T and Gillespie, Marc E and Stein,
Lincoln D and Hermjakob, Henning and D'Eustachio, Peter and
Saez-Rodriguez, Julio and Dopazo, Joaquin and Valencia,
Alfonso and Kitano, Hiroaki and Barillot, Emmanuel and
Auffray, Charles and Balling, Rudi and Schneider, Reinhard},
collaboration = {Community, COVID-19 Disease Map},
title = {{COVID}19 {D}isease {M}ap, a computational knowledge
repository of virus-host interaction mechanisms.},
journal = {Molecular systems biology},
volume = {17},
number = {10},
issn = {1744-4292},
address = {Heidelberg},
publisher = {EMBO Press},
reportid = {DZNE-2021-01564},
pages = {e10387},
year = {2021},
note = {(CC BY)},
abstract = {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.},
keywords = {COVID-19 Drug Treatment / Antiviral Agents: therapeutic use
/ COVID-19: drug therapy / COVID-19: genetics / COVID-19:
immunology / COVID-19: virology / Computational Biology:
methods / Computer Graphics / Cytokines: genetics /
Cytokines: immunology / Data Mining: statistics $\&$
numerical data / Databases, Factual / Gene Expression
Regulation / Host Microbial Interactions: genetics / Host
Microbial Interactions: immunology / Humans / Immunity,
Cellular: drug effects / Immunity, Humoral: drug effects /
Immunity, Innate: drug effects / Lymphocytes: drug effects /
Lymphocytes: immunology / Lymphocytes: virology / Metabolic
Networks and Pathways: genetics / Metabolic Networks and
Pathways: immunology / Myeloid Cells: drug effects / Myeloid
Cells: immunology / Myeloid Cells: virology / Protein
Interaction Mapping / SARS-CoV-2: drug effects / SARS-CoV-2:
genetics / SARS-CoV-2: immunology / SARS-CoV-2:
pathogenicity / Signal Transduction / Software /
Transcription Factors: genetics / Transcription Factors:
immunology / Viral Proteins: genetics / Viral Proteins:
immunology / computable knowledge repository (Other) /
large-scale biocuration (Other) / omics data analysis
(Other) / open access community effort (Other) / systems
biomedicine (Other) / Antiviral Agents (NLM Chemicals) /
Cytokines (NLM Chemicals) / Transcription Factors (NLM
Chemicals) / Viral Proteins (NLM Chemicals)},
cin = {AG Kempermann 1},
ddc = {570},
cid = {I:(DE-2719)1710001},
pnm = {352 - Disease Mechanisms (POF4-352)},
pid = {G:(DE-HGF)POF4-352},
typ = {PUB:(DE-HGF)16},
pubmed = {pmid:34664389},
pmc = {pmc:PMC8524328},
doi = {10.15252/msb.202110387},
url = {https://pub.dzne.de/record/162909},
}
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