scholarly journals Systematic Organization of COVID-19 Data Supported by the Adverse Outcome Pathway Framework

Author(s):  
Penny Nymark ◽  
Magdalini Sachana ◽  
Sofia Batista-Leite ◽  
Jukka Sund ◽  
Catharine E Krebs ◽  
...  

Adverse Outcome Pathways (AOP) provide structured frameworks for systematic organization of research data and knowledge. The AOP framework follows a set of key principles that allow for broad application across diverse disciplines related to human health, including toxicology, pharmacology, virology and medical research. The COVID-19 pandemic engages a great number of scientists world-wide and data is increasing with exponential speed. Diligent data management strategies are employed but approaches for systematically organizing the data-derived information and knowledge are lacking. We believe AOPs can play an important role in improving interpretation and efficient application of scientific understanding of COVID-19. Here, we outline a newly initiated effort to streamline collaboration between scientists across the world towards development of AOPs for COVID-19, and describe the overarching aims of the effort, as well as the expected outcomes and research support that they will provide.

2021 ◽  
Vol 9 ◽  
Author(s):  
Penny Nymark ◽  
Magdalini Sachana ◽  
Sofia Batista Leite ◽  
Jukka Sund ◽  
Catharine E. Krebs ◽  
...  

Adverse Outcome Pathways (AOP) provide structured frameworks for the systematic organization of research data and knowledge. The AOP framework follows a set of key principles that allow for broad application across diverse disciplines related to human health, including toxicology, pharmacology, virology and medical research. The COVID-19 pandemic engages a great number of scientists world-wide and data is increasing with exponential speed. Diligent data management strategies are employed but approaches for systematically organizing the data-derived information and knowledge are lacking. We believe AOPs can play an important role in improving interpretation and efficient application of scientific understanding of COVID-19. Here, we outline a newly initiated effort, the CIAO project (https://www.ciao-covid.net/), to streamline collaboration between scientists across the world toward development of AOPs for COVID-19, and describe the overarching aims of the effort, as well as the expected outcomes and research support that they will provide.


2019 ◽  
Author(s):  
Adrienne Canino

This essay examines the beta tool from Google, Google Dataset Search. The Google Dataset Search, announced in September 2018, is a search engine specific to finding research data published on the internet. The structure and methods of the search engine are examined, as well as the methods Google recommends to web developers to make it an effective tool across the World Wide Web. The column concludes with a discussion of the pros and cons of this tool in the research information landscape.


2020 ◽  
Author(s):  
Maria Elenius ◽  
Alena Bartosova ◽  
Jude Musuuza ◽  
Berit Arheimer

<p>Irrigation practices of various kinds are used in farming all over the world. Especially in cases of over-irrigation and inadequate drainage, evaporation losses can be high and lead to accumulation of minerals in the soils. Water uptake in crops is driven by osmosis, and as such it is reduced or diminished when salt concentrations in the soil water increase. Today, approximately 10 % of irrigated land worldwide has faced diminished production due to salinization, and losses increase every year. There is also concern that global warming can deteriorate production further due to increased evaporation, which should be considered in the light of increasing crop demands with population growth. There is therefore pressing concern to study effects and measures on a global scale.</p><p>Continental to global scale hydrological models have emerged in recent years as tools for flood forecasting and estimation of dynamic water fluxes. HYPE is a catchment-based model that simulates rainfall-runoff as well as water quality processes. Recently, an application was developed based on HYPE that covers almost the entire globe, World Wide HYPE (Arheimer et al., 2019). This tool also has great potential for future global assessments of soil salinization under different scenarios.</p><p>In this work, a salinization routine was developed in HYPE, whereby salt components follow all main natural hydrological pathways as well as irrigation using groundwater or river flow as a water source. Equilibrium reactions, complexation and cation exchange determine the distribution between dissolved and solid states in the soil. A semi-arid catchment in South Africa with salinization issues (the Crocodile River, Mpumalanga province) was chosen for code development, calibration and verification. Evaluations were based on comparison of simulated and observed mineral concentrations in rivers and groundwater. The model was also tested for all of South Africa.</p><p>Detailed analyses of the soil salinity processes were carried out for the Crocodile River catchment. Results show the sensitivity of salinization to hydrological parameters such as recession coefficients, infiltration capacities and macropore flow. This will guide future calibration of the World Wide HYPE model setup. Assessment of the major processes and sources of salinization is performed, and mitigation strategies such as irrigation control and drainage management are tested. Possible regionalization of parameters for global salinization modeling is also suggested based on the results.</p><p>Arheimer, B., Pimentel, R., Isberg, K., Crochemore, L., Andersson, J. C. M., Hasan, A., and Pineda, L. (accepted). Global catchment modelling using World-Wide HYPE (WWH), open data and stepwise parameter estimation, Hydrol. Earth Syst. Sci, https://doi.org/10.5194/hess-2019-111, in press, 2019</p>


Author(s):  
Youngjun kim ◽  
Chang Gyun Park ◽  
Sang Rak Lim ◽  
Indong Jun ◽  
Yong Oh Lee

Increasing global concern over COVID-19 has recently brought greater attention to studies due to the ease of person-to-person transmission and the current lack of effective antiviral therapy. Here, we proposed the application of the adverse outcome pathway (AOP) framework to support re-search on the pathogenesis of viral disease. We first constructed adverse outcome pathways (AOPs) applicable to COVID-19 management to understand whether the infection causes severe acute respiratory distress. Based on the AOP framework where mechanistic elucidation of the pathway from the interaction of chemicals (or viruses) to apical endpoints is represented, our COVID-19 AOP indicated that the molecular initiating event (MIE) was angiotensin-converting enzyme 2 (ACE2) interaction, and the key events (KEs) were the increased pro-inflammatory cytokines in immune cells, with increased mortality as an apical adverse outcome (AO). However, there is still limited information on the toxicity mechanisms of AOPs in COVID-19; therefore, detailed KEs and AOs on toxicity mechanisms will be required to fill these gaps in the data. This study demonstrated that the COVID-19 AOP framework is a suitable tool to design new drugs and to integrate crowded-sourced information for the battle against the COVID-19 pandemic.


2021 ◽  
Author(s):  
Marvin Martens ◽  
Chris Evelo ◽  
Egon Willighagen

<div>The AOP-Wiki is the main environment for the development and storage of Adverse Outcome Pathways. These Adverse Outcome Pathways describe mechanistic information about toxicodynamic processes and can be used to develop effective risk assessment strategies. However, it is challenging to automatically and systematically parse, filter, and use its contents. We explored solutions to better structure the AOP-Wiki content and to link it with chemical and biological resources. Together this allows more detailed exploration which can be automated.</div><div><br></div><div>We converted the complete AOP-Wiki content into Resource Description Framework. We used over twenty ontologies for the semantic annotation of property-object relations, including the ChemInformatics Ontology, Dublin Core, and the Adverse Outcome Pathway Ontology. The latter was used over 8,000 times. Furthermore, over 3,500 link-outs were added to twelve chemical databases and over 6,500 link-outs to four gene and protein databases. </div><div><br></div><div>SPARQL queries can be used against the Resource Description Framework to answer biological and toxicological questions, such as listing measurement methods for all Key Events leading to an Adverse Outcome of interest. The full power that the use of this new resource provides becomes apparent when combining the content with external databases using federated queries. For example, we can link genes related to Key Events with molecular pathway on WikiPathways in which they occur and find all Adverse Outcome Pathways caused by stressors that are part of a particular chemical group. Overall, the AOP-Wiki Resource Description Framework allows new ways to explore the rapidly growing Adverse Outcome Pathway knowledge and makes the integration of this database in automated workflows possible.</div>


2021 ◽  
Vol 69 (4. ksz.) ◽  
pp. 121-124
Author(s):  
Viktor Németh

The MIT Press Essential Knowledge series provides the reader with accessible, concise, yet interesting and completely up-to-date information. Each part was written by excellent experts on the subject, in a language understood by non-experts, too. In this way, the current research data and results in the field of each topic can be really used. Nowadays, it is not easy to find in the endless set of information obtainable on the World Wide Web those that essentially provide the fundamental knowledge on a particular topic. The MIT series fill a gap in this. The topic of the present volume of the series is the anticorruption, as a world phenomenon, its current development and situation. And the topicality of the current theme is perhaps duly justified by the following World Bank estimate: “Much of the globe is infected with corruption, sapping as much as 3 percent of annual per capita GDP in large swathes of Africa, Asia, and Latin America. Even North America is hardly immune. The World Bank says that $1 trillion or more is lost each year to corruption, globally.” (Rotberg, 2020).


2021 ◽  
Author(s):  
Marvin Martens ◽  
Chris Evelo ◽  
Egon Willighagen

<div>The AOP-Wiki is the main environment for the development and storage of Adverse Outcome Pathways. These Adverse Outcome Pathways describe mechanistic information about toxicodynamic processes and can be used to develop effective risk assessment strategies. However, it is challenging to automatically and systematically parse, filter, and use its contents. We explored solutions to better structure the AOP-Wiki content and to link it with chemical and biological resources. Together this allows more detailed exploration which can be automated.</div><div><br></div><div>We converted the complete AOP-Wiki content into Resource Description Framework. We used over twenty ontologies for the semantic annotation of property-object relations, including the ChemInformatics Ontology, Dublin Core, and the Adverse Outcome Pathway Ontology. The latter was used over 8,000 times. Furthermore, over 3,500 link-outs were added to twelve chemical databases and over 6,500 link-outs to four gene and protein databases. </div><div><br></div><div>SPARQL queries can be used against the Resource Description Framework to answer biological and toxicological questions, such as listing measurement methods for all Key Events leading to an Adverse Outcome of interest. The full power that the use of this new resource provides becomes apparent when combining the content with external databases using federated queries. For example, we can link genes related to Key Events with molecular pathway on WikiPathways in which they occur and find all Adverse Outcome Pathways caused by stressors that are part of a particular chemical group. Overall, the AOP-Wiki Resource Description Framework allows new ways to explore the rapidly growing Adverse Outcome Pathway knowledge and makes the integration of this database in automated workflows possible.</div>


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