COVID-19 Disease Map, a computational knowledge repository of SARS-CoV-2 virus-host interaction mechanisms
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Abstract
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. We discuss the tools, platforms, and guidelines necessary for the distributed development of its contents by a multi-faceted community of biocurators, domain experts, bioinformaticians, and computational biologists. We highlight the role of relevant databases and text mining approaches in enrichment and validation of the curated mechanisms. We describe the contents of the Map and their relevance to the molecular pathophysiology of COVID-19 and the analytical and computational modelling approaches that can be applied for mechanistic data interpretation and predictions. We conclude by demonstrating concrete applications of our work through several use cases and highlight new testable hypotheses.
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SciScore for 10.1101/2020.10.26.356014: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Table 2: Resources
No key resources detected.
Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.Results from TrialIdentifier: No clinical trial numbers were referenced.
Results from Barzooka: We did not find any issues relating to the usage of bar …
SciScore for 10.1101/2020.10.26.356014: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Table 2: Resources
No key resources detected.
Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.Results from TrialIdentifier: No clinical trial numbers were referenced.
Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
Results from JetFighter: We did not find any issues relating to colormaps.
Results from rtransparent:- Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
- Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
- No protocol registration statement was detected.
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SciScore for 10.1101/2020.10.26.356014: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Table 2: Resources
Software and Algorithms Sentences Resources Technische Universität München, Center for Mathematics, Chair of Mathematical Modeling of Biological Systems, 85748 Mathematical Modeling of Biological Systemssuggested: (National University of Singapore, Computational Bioengineering Laboratory, RRID:SCR_000284)3] Interaction No Yes No No Elsevier Pathway Collection14 Pathway Yes Yes Yes Yes9 10 … SciScore for 10.1101/2020.10.26.356014: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Table 2: Resources
Software and Algorithms Sentences Resources Technische Universität München, Center for Mathematics, Chair of Mathematical Modeling of Biological Systems, 85748 Mathematical Modeling of Biological Systemssuggested: (National University of Singapore, Computational Bioengineering Laboratory, RRID:SCR_000284)3] Interaction No Yes No No Elsevier Pathway Collection14 Pathway Yes Yes Yes Yes9 10 https://www.semanticscholar.org/cord19/download (accessed on 20.10.2020) 11 https://data.mendeley.com/datasets/h9vs5s8fz2/draft?a=f40961bb-9798-4fd1-8025-e2a3ba47b02e 12 https://www.imexconsortium.org 13 https://signor.uniroma2.it/covid/ 14 https://pathwaystudio.com bioRxiv preprint doi: https://doi.org/10.1101/2020.10.26.356014; this version posted October 28, 2020. https://www.imexconsortium.orgsuggested: (IMEx - The International Molecular Exchange Consortium, RRID:SCR_002805)This pipeline was applied to the CORD-19 dataset and the collection of MEDLINE abstracts associated with the genes in the SARS-CoV-2 PPI network [34] using the Entrez Gene Reference-Into-Function (GeneRIF). Entrez Genesuggested: (Entrez Gene, RRID:SCR_002473)Finally, INDRA 15 https://biokb.lcsb.uni.lu 16 https://ailani.ai/cgi/login_bioxm_portal.cgi 17 https://git-r3lab.uni.lu/covid/models/-/tree/master/Resources/Text%20mining 18 https://opennlp.apache.org 19 https://rupertoverall.net/covidminer bioRxiv preprint doi: https://doi.org/10.1101/2020.10.26.356014; this version posted October 28, 2020. bioRxivsuggested: (bioRxiv, RRID:SCR_003933)These can then be used directly for activity simulations using the BioLayout network analysis tool [309]. BioLayoutsuggested: (BioLayout Express 3D, RRID:SCR_007179)Results from OddPub: Thank you for sharing your data.
Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.
Results from TrialIdentifier: No clinical trial numbers were referenced.
Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
Results from JetFighter: We did not find any issues relating to colormaps.
About SciScore
SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
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