scholarly journals A protocol for adding knowledge to Wikidata: aligning resources on human coronaviruses

BMC Biology ◽  
2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Andra Waagmeester ◽  
Egon L. Willighagen ◽  
Andrew I. Su ◽  
Martina Kutmon ◽  
Jose Emilio Labra Gayo ◽  
...  
Keyword(s):  
Common Ground ◽  
Knowledge Bases ◽  
Public Knowledge ◽  
Medical Problems ◽  
Human Coronavirus ◽  
Data Schema ◽  
Helping Others ◽  
Human Coronaviruses ◽  
The Right ◽  
Human Coronavirus 229E

Abstract Background Pandemics, even more than other medical problems, require swift integration of knowledge. When caused by a new virus, understanding the underlying biology may help finding solutions. In a setting where there are a large number of loosely related projects and initiatives, we need common ground, also known as a “commons.” Wikidata, a public knowledge graph aligned with Wikipedia, is such a commons and uses unique identifiers to link knowledge in other knowledge bases. However, Wikidata may not always have the right schema for the urgent questions. In this paper, we address this problem by showing how a data schema required for the integration can be modeled with entity schemas represented by Shape Expressions. Results As a telling example, we describe the process of aligning resources on the genomes and proteomes of the SARS-CoV-2 virus and related viruses as well as how Shape Expressions can be defined for Wikidata to model the knowledge, helping others studying the SARS-CoV-2 pandemic. How this model can be used to make data between various resources interoperable is demonstrated by integrating data from NCBI (National Center for Biotechnology Information) Taxonomy, NCBI Genes, UniProt, and WikiPathways. Based on that model, a set of automated applications or bots were written for regular updates of these sources in Wikidata and added to a platform for automatically running these updates. Conclusions Although this workflow is developed and applied in the context of the COVID-19 pandemic, to demonstrate its broader applicability it was also applied to other human coronaviruses (MERS, SARS, human coronavirus NL63, human coronavirus 229E, human coronavirus HKU1, human coronavirus OC4).

scholarly journals A protocol for adding knowledge to Wikidata, a case report

2020 ◽  
Author(s):  
Andra Waagmeester ◽  
Egon L. Willighagen ◽  
Andrew I Su ◽  
Martina Kutmon ◽  
Jose Emilio Labra Gayo ◽  
...  
Keyword(s):  
Common Ground ◽  
Knowledge Bases ◽  
Public Knowledge ◽  
Medical Problems ◽  
Human Coronavirus ◽  
Data Schema ◽  
Helping Others ◽  
Human Coronaviruses ◽  
The Right ◽  
Human Coronavirus 229E

AbstractPandemics, even more than other medical problems, require swift integration of knowledge. When caused by a new virus, understanding the underlying biology may help finding solutions. In a setting where there are a large number of loosely related projects and initiatives, we need common ground, also known as a “commons”. Wikidata, a public knowledge graph aligned with Wikipedia, is such a commons and uses unique identifiers to link knowledge in other knowledge bases However, Wikidata may not always have the right schema for the urgent questions. In this paper, we address this problem by showing how a data schema required for the integration can be modelled with entity schemas represented by Shape Expressions. As a telling example, we describe the process of aligning resources on the genomes and proteomes of the SARS-CoV-2 virus and related viruses as well as how Shape Expressions can be defined for Wikidata to model the knowledge, helping others studying the SARS-CoV-2 pandemic. How this model can be used to make data between various resources interoperable, is demonstrated by integrating data from NCBI Taxonomy, NCBI Genes, UniProt, and WikiPathways. Based on that model, a set of automated applications or bots were written for regular updates of these sources in Wikidata and added to a platform for automatically running these updates. Although this workflow is developed and applied in the context of the COVID-19 pandemic, to demonstrate its broader applicability it was also applied to other human coronaviruses (MERS, SARS, Human Coronavirus NL63, Human coronavirus 229E, Human coronavirus HKU1, Human coronavirus OC4).

scholarly journals Analysis of human coronavirus 229E spike and nucleoprotein genes demonstrates genetic drift between chronologically distinct strains

2006 ◽  
Vol 87 (5) ◽  
pp. 1203-1208 ◽  
Author(s):  
Doris Chibo ◽  
Chris Birch
Keyword(s):  
Phylogenetic Analysis ◽  
Respiratory Infections ◽  
N Gene ◽  
Human Coronavirus ◽  
S Gene ◽  
Limited Variation ◽  
Contrast Analysis ◽  
Human Coronaviruses ◽  
Human Coronavirus 229E ◽  
S Genes

Historically, coronaviruses have been recognized as a cause of minor respiratory infections in humans. However, the recent identification of three novel human coronaviruses, one causing severe acute respiratory syndrome (SARS), has prompted further examination of these viruses. Previous studies of geographically and chronologically distinct Human coronavirus 229E (HCoV-229E) isolates have found only limited variation within S gene nucleotide sequences. In contrast, analysis of the S genes of contemporary Human coronavirus OC43 variants identified in Belgium revealed two distinct viruses circulating during 2003 and 2004. Here, the S and N gene sequences of 25 HCoV-229E variants identified in Victoria, Australia, between 1979 and 2004 in patients with symptomatic infections were determined. Phylogenetic analysis showed clustering of the isolates into four groups, with evidence of increasing divergence with time. Evidence of positive selection in the S gene was also established.

scholarly journals BRIEF FACTS ABOUT COVID-19 (SARS-CoV-2) and DETAILS

2021 ◽  
Author(s):  
Sorush Niknamian
Keyword(s):  
Respiratory Tract ◽  
Common Cold ◽  
Respiratory Tract Infections ◽  
Human Coronavirus ◽  
The Family ◽  
The Common ◽  
Human Coronaviruses ◽  
The 1960S ◽  
Tract Infections ◽  
Human Coronavirus 229E

Coronaviruses are a group of related viruses that cause diseases in mammals and birds. In humans, coronaviruses cause respiratory tract infections that can range from mild to lethal. Mild illnesses include some cases of the common cold, while more lethal varieties can cause SARS, MERS, and COVID-19. The outbreak was identified in Wuhan, China, in December 2019, declared to be a Public Health Emergency of International Concern on 30 January 2020, and recognized as a pandemic on 11 March 2020. Coronaviruses are the subfamily Orthocoronavirinae, within the family of Coronaviridae, order Nidovirales, and realm Riboviria. They are enveloped viruses with a positive-sense single-stranded RNA genome and a nucleocapsid of helical symmetry. The genome size of coronaviruses is approximately from 26 to 32 kilobases. Coronaviruses were first discovered in the 1930s and Human coronaviruses were discovered in the 1960s. The earliest ones studied were from human patients with the common cold, which were later named human coronavirus 229E and human coronavirus OC43. Other human coronaviruses have since been identified, including SARS-CoV in 2003, HCoV NL63 in 2004, HKU1 in 2005, MERS-CoV in 2012, and SARS-CoV-2 in 2019. Most of these have involved serious respiratory tract infections

scholarly journals Brief Facts about COVID-19 (SARS-CoV-2)

2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Sorush Niknamian
Keyword(s):  
Respiratory Tract ◽  
Common Cold ◽  
Respiratory Tract Infections ◽  
Human Coronavirus ◽  
The Family ◽  
The Common ◽  
Human Coronaviruses ◽  
The 1960S ◽  
Tract Infections ◽  
Human Coronavirus 229E

Coronaviruses are a group of related viruses that cause diseases in mammals and birds. In humans, coronaviruses cause respiratory tract infections that can range from mild to lethal. Mild illnesses include some cases of the common cold, while more lethal varieties can cause SARS, MERS, and COVID-19. The outbreak was identified in Wuhan, China, in December 2019, declared to be a Public Health Emergency of International Concern on 30 January 2020, and recognized as a pandemic on 11 March 2020. Coronaviruses are the subfamily Orthocoronavirinae, within the family of Coronaviridae, order Nidovirales, and realm Riboviria. They are enveloped viruses with a positive-sense single-stranded RNA genome and a nucleocapsid of helical symmetry. The genome size of coronaviruses is approximately from 26 to 32 kilobases. Coronaviruses were first discovered in the 1930s and Human coronaviruses were discovered in the 1960s. The earliest ones studied were from human patients with the common cold, which were later named human coronavirus 229E and human coronavirus OC43. Other human coronaviruses have since been identified, including SARS-CoV in 2003, HCoV NL63 in 2004, HKU1 in 2005, MERS-CoV in 2012, and SARS-CoV-2 in 2019. Most of these have involved serious respiratory tract infections

The Seasonal End of Human Coronavirus Hospital Admissions with Implications for SARS-CoV-2 (Preprint)

2020 ◽  
Author(s):  
Alan T Evangelista
Keyword(s):  
Hospital Admissions ◽  
Disease Incidence ◽  
Influenza Viruses ◽  
Seasonal Effects ◽  
Human Coronavirus ◽  
Enveloped Virus ◽  
Multiplex Pcr Assay ◽  
Contact Transmission ◽  
Human Coronaviruses

UNSTRUCTURED The seasonality of influenza viruses and endemic human coronaviruses was tracked over an 8-year period to assess key epidemiologic reduction points in disease incidence for an urban area in the northeast United States. Patients admitted to a pediatric hospital with worsening respiratory symptoms were tested using a multiplex PCR assay from nasopharyngeal swabs. The additive seasonal effects of outdoor temperatures and indoor relative humidity (RH) were evaluated. The 8-year average peak activity of human coronaviruses occurred in the first week of January, when droplet and contact transmission was enabled by the low indoor RH of 20-30%. Previous studies have shown that an increase in RH to 50% has been associated with markedly reduced viability and transmission of influenza virus and animal coronaviruses. As disease incidence was reduced by 50% in early March, to 75% in early April, to greater than 99% at the end of April, a relationship was observed from colder temperatures in January with a low indoor RH to a gradual increase in outdoor temperatures in April with an indoor RH of 45-50%. As a lipid-bound, enveloped virus with similar size characteristics to endemic human coronaviruses, SARS-CoV-2 should be subject to the same dynamics of reduced viability and transmission with increased humidity. In addition to the major role of social distancing, the transition from lower to higher indoor RH with increasing outdoor temperatures could have an additive effect on the decrease in SARS-CoV-2 cases in May. Over the 8-year period of this study, human coronavirus activity was either zero or >99% reduction in the months of June through September, and the implication would be that SARS-Cov-2 may follow a similar pattern. INTERNATIONAL REGISTERED REPORT RR2-doi.org/10.1101/2020.05.15.20103416

The Taubman/Golandsky Approach to the Violin

Public Voices ◽  
2016 ◽  
Vol 12 (2) ◽  
pp. 7
Author(s):  
Sophie Till
Keyword(s):  
The Other ◽  
Technical Approach ◽  
Piano Technique ◽  
Pedagogical Approach ◽  
New Developments ◽  
Body Of Knowledge ◽  
Music Making ◽  
Helping Others ◽  
The One ◽  
The Right

Three years ago Sophie Till started working with pianist Edna Golandsky, the leading exponent of the Taubman Piano Technique, an internationally acclaimed approach that is well known to pianists, on the one hand, for allowing pianists to attain a phenomenal level of virtuosity and on the other, for solving very serious piano-related injuries. Till, a violinist, quickly realized that here was a unique technical approach that could not only identify and itemize the minute movements that underlie a virtuoso technique but could show how these movements interact and go into music making at the highest level. Furthermore, through the work of the Golandsky Institute, she saw a pedagogical approach that had been developed to a remarkable depth and level of clarity. It was an approach that had the power to communicate in a way she had never seen before, despite her own first class violin training from the earliest age. While the geography and “look” on the violin are different from the piano, the laws governing coordinate motion specifically in playing the instrument are the same for pianists and violinists. As a result of Till’s work translating the technique for violin, a new pedagogical approach for violinists of all ages is emerging; the Taubman/Golandsky Approach to the Violin. In reflecting on these new developments, Edna Golandsky wrote, “I have been working with the Taubman Approach for more than 30 years and have worked regularly with other instrumentalists. However, Sophie Till was the first violinist who asked me to teach her with the same depth that I do with pianists. With her conceptual and intellectual agility as well as complete dedication to helping others, she has been the perfect partner to translate this body of knowledge for violinists. Through this collaboration, Sophie is helping develop a new ‘language’ for violinist that will prevent future problems, solve present ones and start beginners on the right road to becoming the best they can be. The implications of this new work for violinists are enormous.”

scholarly journals Natural and Nature-Derived Products Targeting Human Coronaviruses

Molecules ◽  
2021 ◽  
Vol 26 (2) ◽  
pp. 448
Author(s):  
Konstantina Vougogiannopoulou ◽  
Angela Corona ◽  
Enzo Tramontano ◽  
Michael N. Alexis ◽  
Alexios-Leandros Skaltsounis
Keyword(s):  
Natural Products ◽  
Antiviral Agents ◽  
Critical Perspective ◽  
Human Coronavirus ◽  
State Of Emergency ◽  
Pharmacological Agents ◽  
Pure Compounds ◽  
Total Plant ◽  
Human Coronaviruses ◽  
The 1960S

The ongoing pandemic of severe acute respiratory syndrome (SARS), caused by the SARS-CoV-2 human coronavirus (HCoV), has brought the international scientific community before a state of emergency that needs to be addressed with intensive research for the discovery of pharmacological agents with antiviral activity. Potential antiviral natural products (NPs) have been discovered from plants of the global biodiversity, including extracts, compounds and categories of compounds with activity against several viruses of the respiratory tract such as HCoVs. However, the scarcity of natural products (NPs) and small-molecules (SMs) used as antiviral agents, especially for HCoVs, is notable. This is a review of 203 publications, which were selected using PubMed/MEDLINE, Web of Science, Scopus, and Google Scholar, evaluates the available literature since the discovery of the first human coronavirus in the 1960s; it summarizes important aspects of structure, function, and therapeutic targeting of HCoVs as well as NPs (19 total plant extracts and 204 isolated or semi-synthesized pure compounds) with anti-HCoV activity targeting viral and non-viral proteins, while focusing on the advances on the discovery of NPs with anti-SARS-CoV-2 activity, and providing a critical perspective.

scholarly journals Examining the persistence of human Coronavirus 229E on fresh produce

2021 ◽  
pp. 103780
Author(s):  
Madeleine Blondin-Brosseau ◽  
Jennifer Harlow ◽  
Tanushka Doctor ◽  
Neda Nasheri
Keyword(s):  
Fresh Produce ◽  
Human Coronavirus ◽  
Human Coronavirus 229E

Effect of pH and temperature on the infectivity of human coronavirus 229E

1989 ◽  
Vol 35 (10) ◽  
pp. 972-974 ◽  
Author(s):  
Alain Lamarre ◽  
Pierre J. Talbot
Keyword(s):  
Incubation Period ◽  
Storage Conditions ◽  
Viral Infectivity ◽  
Human Coronavirus ◽  
Virus Growth ◽  
The Stability ◽  
And Storage ◽  
Influence Of Ph ◽  
Human Coronavirus 229E

The stability of human coronavirus 229E infectivity was maximum at pH 6.0 when incubated at either 4 or 33 °C. However, the influence of pH was more pronounced at 33 °C. Viral infectivity was completely lost after a 14-day incubation period at 22, 33, or 37 °C but remained relatively constant at 4 °C for the same length of time. Finally, the infectious titer did not show any significant reduction when subjected to 25 cycles of thawing and freezing. These studies will contribute to optimize virus growth and storage conditions, which will facilitate the molecular characterization of this important pathogen.Key words: coronavirus, pH, temperature, infectivity, human coronavirus.

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