Cov19VaxKB: A Web-based Integrative COVID-19 Vaccine Knowledge Base.
Ontology highlight
ABSTRACT:
SUBMITTER: Huang PC
PROVIDER: S-EPMC8716025 | biostudies-literature | 2021 Dec
REPOSITORIES: biostudies-literature
Publications
Cov19VaxKB: A Web-based Integrative COVID-19 Vaccine Knowledge Base.
Huang Philip C PC Goru Rohit R Huffman Anthony A Yu Lin Asiyah A Cooke Michael F MF He Yongqun Y
Vaccine: X 20211228
The development of SARS-CoV-2 vaccines during the COVID-19 pandemic has prompted the emergence of COVID-19 vaccine data. Timely access to COVID-19 vaccine information is crucial to researchers and public. To support more comprehensive annotation, integration, and analysis of COVID-19 vaccine information, we have developed Cov19VaxKB, a knowledge-focused COVID-19 vaccine database (http://www.violinet.org/cov19vaxkb/). Cov19VaxKB features comprehensive lists of COVID-19 vaccines, vaccine formulati ...[more]
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Project description:BackgroundCoronavirus disease 2019 or COVID-19 is caused by a newly discovered coronavirus, SARS-CoV-2. The Malaysian government has planned to procure COVID-19 vaccine through multiple agencies and companies in order to vaccinate at least 70% of the population. This study aimed to determine the knowledge, acceptance and perception of Malaysian adults regarding the COVID-19 vaccine.MethodologyAn online survey was conducted for two weeks in December 2020. A bilingual, semi-structured questionnaire was set up using Google Forms and the generated link was shared on social media (i.e., Facebook and WhatsApp). The questionnaire consisted of questions on knowledge, acceptance and perception of COVID-19 vaccine. The association between demographic factors with scores on knowledge about COVID-19 vaccine were analysed using the Mann-Whitney test for two categorical variables, and the Kruskal-Wallis test used for more than two categorical variables.ResultsA total of 1406 respondents participated, with the mean age of 37.07 years (SD = 16.05) years, and among them 926 (65.9%) were female. Sixty two percent of respondents had poor knowledge about COVID-19 vaccine (mean knowledge score 4.65; SD = 2.32) and 64.5% were willing to get a COVID-19 vaccine. High knowledge scores associated with higher education background, higher-income category and living with who is at higher risk of getting severe COVID-19. They were more likely to be willing to get vaccinated if they were in a lower age group, have higher education levels and were female.ConclusionEven though knowledge about vaccine COVID-19 is inadequate, the majority of the respondents were willing to get vaccinated. This finding can help the Ministry of Health plan for future efforts to increase vaccine uptake that may eventually lead to herd immunity against COVID-19.
| S-EPMC8362951 | biostudies-literature
Project description:BioBIKE (biobike.csbc.vcu.edu) is a web-based environment enabling biologists with little programming expertise to combine tools, data, and knowledge in novel and possibly complex ways, as demanded by the biological problem at hand. BioBIKE is composed of three integrated components: a biological knowledge base, a graphical programming interface and an extensible set of tools. Each of the five current BioBIKE instances provides all available information (genomic, metabolic, experimental) appropriate to a given research community. The BioBIKE programming language and graphical programming interface employ familiar operations to help users combine functions and information to conduct biologically meaningful analyses. Many commonly used tools, such as Blast and PHYLIP, are built-in, allowing users to access them within the same interface and to pass results from one to another. Users may also invent their own tools, packaging complex expressions under a single name, which is immediately made accessible through the graphical interface. BioBIKE represents a partial solution to the difficult question of how to enable those with no background in computer programming to work directly and creatively with mass biological information. BioBIKE is distributed under the MIT Open Source license. A description of the underlying language and other technical matters is available at www.Biobike.org.
| S-EPMC2703918 | biostudies-literature
Project description:BackgroundCOVID-19 is a highly transmissible illness caused by SARS-CoV-2. The disease has affected more than 200 countries, and the measures that have been implemented to combat its spread, as there is still no vaccine or definitive medication, have been based on supportive interventions and drug repositioning. Brazil, the largest country in South America, has had more than 140,000 recorded deaths and is one of the most affected countries. Despite the extensive quantity of scientifically recognized information, there are still conflicting discussions on how best to face the disease and the virus, especially with regard to social distancing, preventive methods, and the use of medications.ObjectiveThe main purpose of this study is to evaluate the Brazilian population's basic knowledge about COVID-19 to demonstrate how Brazilians are managing to identify scientifically proven information.MethodsA cross-sectional study design was used. An original online questionnaire survey was administered from June 16 to August 21, 2020, across all five different geopolitical regions of the country (ie, the North, Northeast, Center-West, Southeast, and South). The questionnaire was comprised of questions about basic aspects of COVID-19, such as the related symptoms, conduct that should be followed when suspected of infection, risk groups, prevention, transmission, and social distancing. The wrong questionnaire response alternatives were taken from the fake news combat website of the Brazilian Ministry of Health. Participants (aged ≥18 years) were recruited through social networking platforms, including Facebook, WhatsApp, and Twitter. The mean distributions, frequencies, and similarities or dissimilarities between the responses for the different variables of the study were evaluated. The significance level for all statistical tests was less than .05.ResultsA total of 4180 valid responses representative of all the states and regions of Brazil were recorded. Most respondents had good knowledge about COVID-19, getting an average of 86.59% of the total score with regard to the basic aspects of the disease. The region, education level, age, sex, and social condition had a significant association (P<.001) with knowledge about the disease, which meant that women, the young, those with higher education levels, nonrecipients of social assistance, and more economically and socially developed regions had more correct answers.ConclusionsOverall, Brazilians with social media access have a good level of basic knowledge about COVID-19 but with differences depending on the analyzed subgroup. Due to the limitation of the platform used in carrying out the study, care should be taken when generalizing the study findings to populations with less education or who are not used to accessing social networking platforms.
| S-EPMC7822056 | biostudies-literature
Project description:Objectives Rapid vaccination is the only way to fight against COVID-19.Vaccine hesitancy is the major barrier against this strategy. The main objective of this cross-sectional study was to analyze COVID-19 vaccine acceptance in the general population of West Bengal (India), as well as to investigate the factors that were independently associated with people's desire to receive the vaccine. Methods An online questionnaire was distributed by email, Whatsapp, and other social media platforms, and the responses were analyzed using the SPSS (Version 20) software. Results We conducted a web-based survey in West Bengal, India (N = 803), and accumulated information on individuals' desire to adopt vaccine against COVID-19, views about the virus's effectiveness, and many knowledge-based socio-demographic factors that potentially impact the overall vaccination efforts. We found that, 12.08% of participants do not believe that vaccination against COVID-19 is necessary, but among the rest of the population, 44.33% of individuals are willing to be vaccinated once the vaccine is available, whereas 39.60% of the population responded that they will not be vaccinated immediately but will do so later. Conclusions Despite the participants' strong vaccine willingness, our findings revealed a troubling degree of lake of awareness and insignificant scientific knowledge about the COVID-19 pandemic and its associated vaccination programme. Vaccination hesitancy is not a barrier in this survey region, but poor vaccine availability and a lack of awareness campaigns may instill unfavorable beliefs in those who refuse to be vaccinated.
| S-EPMC9472583 | biostudies-literature
Project description:ObjectivesRapid vaccination is the only way to fight against COVID-19.Vaccine hesitancy is the major barrier against this strategy. The main objective of this cross-sectional study was to analyze COVID-19 vaccine acceptance in the general population of West Bengal (India), as well as to investigate the factors that were independently associated with people's desire to receive the vaccine.MethodsAn online questionnaire was distributed by email, Whatsapp, and other social media platforms, and the responses were analyzed using the SPSS (Version 20) software.ResultsWe conducted a web-based survey in West Bengal, India (N = 803), and accumulated information on individuals' desire to adopt vaccine against COVID-19, views about the virus's effectiveness, and many knowledge-based socio-demographic factors that potentially impact the overall vaccination efforts. We found that, 12.08% of participants do not believe that vaccination against COVID-19 is necessary, but among the rest of the population, 44.33% of individuals are willing to be vaccinated once the vaccine is available, whereas 39.60% of the population responded that they will not be vaccinated immediately but will do so later.ConclusionsDespite the participants' strong vaccine willingness, our findings revealed a troubling degree of lake of awareness and insignificant scientific knowledge about the COVID-19 pandemic and its associated vaccination programme. Vaccination hesitancy is not a barrier in this survey region, but poor vaccine availability and a lack of awareness campaigns may instill unfavorable beliefs in those who refuse to be vaccinated.
| S-EPMC8808715 | biostudies-literature
Project description:In the last two years, the coronavirus disease 19 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been a scientific and social challenge worldwide. Vaccines have been the most effective intervention for reducing virus transmission and disease severity. However, virus genetic variants are still circulating among vaccinated individuals with different symptomatology disease cases. Understanding the protective or disease associated mechanisms in vaccinated individuals is relevant to advance in vaccine development and implementation. To address this objective, serum protein profiles were characterized by quantitative proteomics and data analysis algorithms in four cohorts of vaccinated individuals uninfected and SARS-CoV-2 infected with asymptomatic, nonsevere and severe disease symptomatology. The results showed that immunoglobulins were the most overrepresented proteins in infected cohorts when compared to PCR-negative individuals. The immunoglobulin profile varied between different infected cohorts and correlated with protective or disease associated capacity. Overrepresented immunoglobulins in PCR-positive individuals correlated with protective response against SARS-CoV-2, other viruses, and thrombosis in asymptomatic cases. In nonsevere cases, correlates of protection against SARS-CoV-2 and HBV together with risk of myasthenia gravis and allergy and autoantibodies were observed. Patients with severe symptoms presented risk for allergy, chronic idiopathic thrombocytopenic purpura, and autoantibodies. The analysis of underrepresented immunoglobulins in PCR-positive compared to PCR-negative individuals identified vaccine-induced protective epitopes in various coronavirus proteins including the Spike receptor-binding domain RBD. Non-immunoglobulin proteins were associated with COVID-19 symptoms and biological processes. These results evidence host-associated differences in response to vaccination and the possibility of improving vaccine efficacy against SARS-CoV-2.
2022-10-14 | PXD031969 | Pride
Project description:Vaccination is a key public health strategy that is known to be effective in mitigating the risk of infection and severe disease. However, in the context of the COVID-19 pandemic, the percentage (<50%) of Malaysians who have received a booster for the COVID-19 vaccine has remained stagnant over a year. This study aimed to determine the prevalence of and the factors associated with hesitancy toward the second dose of booster for the COVID-19 vaccine. A web-based cross-sectional study was conducted from August to November 2022. The Oxford Vaccine Hesitancy Scale was used to assess the hesitancy toward the second dose of booster for the COVID-19 vaccine. Simple and multiple factors logistic regressions were used to determine the predictors of hesitancy. A p-value less than 0.05 was considered to be statistically significant. Data from 798 respondents were included in the analysis. The prevalence of hesitancy toward the second booster of the COVID-19 vaccine was 26.7%. The predictors of second-booster hesitancy were older age (AOR = 1.040, 95 CI = 1.022, 1.058), having received the third dose (first booster) because of instruction by the government (AOR = 2.125, 95% CI = 1.380, 3.274), concern about serious long term side effects of the vaccine (AOR = 4.010, 95% CI = 2.218, 7.250), and opinions of close friends and immediate family members that the booster is harmful (AOR = 2.201, 95% CI = 1.280, 3.785). Conversely, factors that appear to reduce vaccine booster hesitancy were acceptance of the third dose due to the high number of cases and the increasing rate of infection (AOR = 0.548, 95% CI = 0.317, 0.947), the belief that the vaccine will decrease the risk of getting the infection (AOR = 0.491, 95% CI = 0.277, 0.870), and opinions of close friends and immediate family members that the booster is helpful (AOR = 0.479, 95% CI = 0.273, 0.840). In conclusion, more than one-fifth of Malaysians were hesitant to take the second booster of the COVID-19 vaccine. This suggests that appropriate steps that increase vaccine acceptance, taking into consideration the findings of the present study, are needed to address this issue and to foster more positive attitudes toward vaccination. The survey was available in three main languages but limited to people with internet access; hence, it would likely be biased toward younger adults and social media users and exclude those with limited or no internet access, in particular older people. Therefore, the results are not representative of the Malaysian population at large and caution should be exercised when interpreting the findings.
| S-EPMC10058917 | biostudies-literature
Project description:Increasingly sophisticated knowledge about RNA structure and function requires an inclusive knowledge representation that facilitates the integration of independently -generated information arising from such efforts as genome sequencing projects, microarray analyses, structure determination and RNA SELEX experiments. While RNAML, an XML-based representation, has been proposed as an exchange format for a select subset of information, it lacks domain-specific semantics that are essential for answering questions that require expert knowledge. Here, we describe an RNA knowledge base (RKB) for structure-based knowledge using RDF/OWL Semantic Web technologies. RKB extends a number of ontologies and contains basic terminology for nucleic acid composition along with context/model-specific structural features such as sugar conformations, base pairings and base stackings. RKB (available at http://semanticscience.org/projects/rkb) is populated with PDB entries and MC-Annotate structural annotation. We show queries to the RKB using description logic reasoning, thus opening the door to question answering over independently-published RNA knowledge using Semantic Web technologies.
| S-EPMC2903721 | biostudies-literature
Project description:ObjectiveThe coronavirus disease 2019 (COVID-19) pandemic has set a precedent for the fastest-produced vaccine as a result of global collaboration and outreach. This study explored Malaysians' acceptance of the COVID-19 vaccine and its associated factors.MethodsA cross-sectional anonymous web-based survey was disseminated to Malaysian adults aged ≥18 years old via social media platforms between July 10, 2020 and August 31, 2020.ResultsIn the analysis of 4,164 complete responses, 93.2% of participants indicated that they would accept the COVID-19 vaccine if it was offered for free by the Malaysian government. The median out-of-pocket cost that participants were willing to pay for a COVID-19 vaccine was Malaysian ringgit (MYR) 100 (interquartile range [IQR], 100) if it was readily available and MYR 150 (IQR, 200) if the supply was limited. Respondents with a low likelihood of vaccine hesitancy had 13 times higher odds of accepting the COVID-19 vaccine (95% confidence interval [CI], 8.69 to 19.13). High perceived risk and severity were also associated with willingness to be vaccinated, with adjusted odds ratios of 2.22 (95% CI, 1.44 to 3.41) and 2.76 (95% CI, 1.87 to 4.09), respectively. Age and ethnicity were the only independent demographic characteristics that predicted vaccine uptake.ConclusionPublic health strategies targeting perceived risk, perceived susceptibility and vaccine hesitancy could be effective in enhancing vaccine uptake.
| S-EPMC8721269 | biostudies-literature
Project description:The SARS-CoV-2 Delta (B.1.617.2) variant is capable of infecting vaccinated persons. An open question remains as to whether deficiencies in specific vaccine-elicited immune responses result in susceptibility to vaccine breakthrough infection. We investigated 55 vaccine breakthrough infection cases (mostly Delta) in Singapore, comparing them against 86 vaccinated close contacts who did not contract infection. Vaccine breakthrough cases showed lower memory B cell frequencies against SARS-CoV-2 receptor binding domain (RBD). Compared to plasma antibodies, antibodies secreted by memory B cells retained a higher fraction of neutralizing properties against the Delta variant. Inflammatory cytokines including IL-1β and TNF were lower in vaccine breakthrough infections than primary infection of similar disease severity, underscoring the usefulness of vaccination in preventing inflammation. This report highlights the importance of memory B cells against vaccine breakthrough, and suggests that lower memory B cell levels may be a correlate of risk for Delta vaccine breakthrough infection.
| S-SCDT-EMM-2021-15227 | biostudies-other