scholarly journals VIPERdb v3.0: a structure-based data analytics platform for viral capsids

2020 ◽  
Vol 49 (D1) ◽  
pp. D809-D816 ◽  
Author(s):  
Daniel Montiel-Garcia ◽  
Nelly Santoyo-Rivera ◽  
Phuong Ho ◽  
Mauricio Carrillo-Tripp ◽  
Charles L Brooks III ◽  
...  
Keyword(s):  
Data Analytics ◽  
Hot Spot ◽  
Data Access ◽  
Specific Information ◽  
Virus Structure ◽  
Viral Capsids ◽  
Machine Leaning ◽  
Virus World ◽  
Service Oriented ◽  
Derived Data

Abstract VIrus Particle ExploreR data base (VIPERdb) (http://viperdb.scripps.edu) is a curated repository of virus capsid structures and a database of structure-derived data along with various virus specific information. VIPERdb has been continuously improved for over 20 years and contains a number of virus structure analysis tools. The release of VIPERdb v3.0 contains new structure-based data analytics tools like Multiple Structure-based and Sequence Alignment (MSSA) to identify hot-spot residues within a selected group of structures and an anomaly detection application to analyze and curate the structure-derived data within individual virus families. At the time of this writing, there are 931 virus structures from 62 different virus families in the database. Significantly, the new release also contains a standalone database called ‘Virus World database’ (VWdb) that comprises all the characterized viruses (∼181 000) known to date, gathered from ICTVdb and NCBI, and their capsid protein sequences, organized according to their virus taxonomy with links to known structures in VIPERdb and PDB. Moreover, the new release of VIPERdb includes a service-oriented data engine to handle all the data access requests and provides an interface for futuristic data analytics using machine leaning applications.

Managing Inconsistencies in Data Grid Environments

2012 ◽  
pp. 303-316
Author(s):  
Ejaz Ahmed ◽  
Nik Bessis ◽  
Peter Norrington ◽  
Yong Yue
Keyword(s):  
Data Access ◽  
Heterogeneous Data ◽  
Data Mapping ◽  
Data Systems ◽  
Grid Environment ◽  
Federated Databases ◽  
Matching Process ◽  
Generic Strategy ◽  
Service Oriented ◽  
Matching Strategy

Much work has been done in the area of data access and integration using various data mapping, matching, and loading techniques. One of the main concerns when integrating data from heterogeneous data sources is data redundancy. The concern is mainly due to the different business contexts and purposes from which the data systems were originally built. A common process for accessing data from integrated databases involves the use of each data source’s own catalogue or metadata schema. In this article, the authors take the view that there is a greater chance of data inconsistencies, such as data redundancies when integrating them within a grid environment as compared to traditional distributed paradigms. The importance of improving the data search and matching process is briefly discussed, and a partial service oriented generic strategy is adopted to consolidate distinct catalogue schemas of federated databases to access information seamlessly. To this end, a proposed matching strategy between structure objects and data values across federated databases in a grid environment is presented.

Managing Inconsistencies in Data Grid Environments

2010 ◽  
Vol 2 (4) ◽  
pp. 51-64 ◽  
Author(s):  
Ejaz Ahmed ◽  
Nik Bessis ◽  
Peter Norrington ◽  
Yong Yue
Keyword(s):  
Data Access ◽  
Heterogeneous Data ◽  
Data Mapping ◽  
Data Systems ◽  
Grid Environment ◽  
Federated Databases ◽  
Matching Process ◽  
Generic Strategy ◽  
Service Oriented ◽  
Matching Strategy

Much work has been done in the area of data access and integration using various data mapping, matching, and loading techniques. One of the main concerns when integrating data from heterogeneous data sources is data redundancy. The concern is mainly due to the different business contexts and purposes from which the data systems were originally built. A common process for accessing data from integrated databases involves the use of each data source’s own catalogue or metadata schema. In this article, the authors take the view that there is a greater chance of data inconsistencies, such as data redundancies when integrating them within a grid environment as compared to traditional distributed paradigms. The importance of improving the data search and matching process is briefly discussed, and a partial service oriented generic strategy is adopted to consolidate distinct catalogue schemas of federated databases to access information seamlessly. To this end, a proposed matching strategy between structure objects and data values across federated databases in a grid environment is presented.

scholarly journals Genomic Data-Sharing Practices

2019 ◽  
Vol 47 (1) ◽  
pp. 31-40 ◽  
Author(s):  
Angela G. Villanueva ◽  
Robert Cook-Deegan ◽  
Jill O. Robinson ◽  
Amy L. McGuire ◽  
Mary A. Majumder
Keyword(s):  
Data Sharing ◽  
Medical Information ◽  
Public Information ◽  
Genomic Data ◽  
Data Access ◽  
Privacy And Security ◽  
Participant Engagement ◽  
Information Commons ◽  
Derived Data

Making data broadly accessible is essential to creating a medical information commons (MIC). Transparency about data-sharing practices can cultivate trust among prospective and existing MIC participants. We present an analysis of 34 initiatives sharing DNA-derived data based on public information. We describe data-sharing practices captured, including practices related to consent, privacy and security, data access, oversight, and participant engagement. Our results reveal that data-sharing initiatives have some distance to go in achieving transparency.

A Service-Oriented Foundation for Big Data

2020 ◽  
Vol 10 (1) ◽  
pp. 1-17
Author(s):  
Zhaohao Sun
Keyword(s):  
Big Data ◽  
Business Intelligence ◽  
Data Analytics ◽  
Big Data Analytics ◽  
Business Analytics ◽  
Technological Characteristics ◽  
Service Oriented ◽  
Technological Level ◽  
Multi Level ◽  
Big Service

This paper provides a service-oriented foundation for big data. The foundation has two parts. Part 1 reveals 10 big characteristics of big data. Part 2 presents a service-oriented framework for big data. The framework has fundamental, technological, and socio-economic levels. The fundamental level has four big fundamental characteristics of big data: big volume, big velocity, big variety, and big veracity. The technological level consists of three big technological characteristics of big data: Big intelligence, big analytics, big infrastructure. The socioeconomic level has three big socioeconomic characteristics of big data: big service, big value, and big market. The article looks at each level of the proposed framework from a service-oriented perspective. The multi-level framework will help organizations and researchers understand how the 10 big characteristics relate to big opportunities, big challenges, and big impacts arising from big data. The proposed approach in this paper might facilitate the research and development of big data, big data analytics, business intelligence, and business analytics.

scholarly journals Geometric description of self-interaction potential in symmetric protein complexes

2019 ◽  
Vol 6 (1) ◽  
Author(s):  
Charly Empereur-Mot ◽  
Hector Garcia-Seisdedos ◽  
Nadav Elad ◽  
Sucharita Dey ◽  
Emmanuel D. Levy
Keyword(s):  
Self Assembly ◽  
Protein Complexes ◽  
Hot Spot ◽  
Point Mutations ◽  
Supramolecular Assembly ◽  
Internal Symmetry ◽  
Crystallographic Structure ◽  
Viral Capsids ◽  
Reliability Estimates ◽  
Order Structures

Abstract Proteins can self-associate with copies of themselves to form symmetric complexes called homomers. Homomers are widespread in all kingdoms of life and allow for unique geometric and functional properties, as reflected in viral capsids or allostery. Once a protein forms a homomer, however, its internal symmetry can compound the effect of point mutations and trigger uncontrolled self-assembly into high-order structures. We identified mutation hot spots for supramolecular assembly, which are predictable by geometry. Here, we present a dataset of descriptors that characterize these hot spot positions both geometrically and chemically, as well as computer scripts allowing the calculation and visualization of these properties for homomers of choice. Since the biological relevance of homomers is not readily available from their X-ray crystallographic structure, we also provide reliability estimates obtained by methods we recently developed. These data have implications in the study of disease-causing mutations, protein evolution and can be exploited in the design of biomaterials.

scholarly journals Decision Framework for Engaging Cloud-Based Big Data Analytics Vendors

2020 ◽  
Vol 22 (4) ◽  
pp. 60-74
Author(s):  
Emmanuel Wusuhon Yanibo Ayaburi ◽  
Michele Maasberg ◽  
Jaeung Lee
Keyword(s):  
Cloud Computing ◽  
Big Data ◽  
Competitive Advantage ◽  
Data Analytics ◽  
Big Data Analytics ◽  
Unique Contribution ◽  
Data Services ◽  
Business Environments ◽  
Digital Era ◽  
Service Oriented

Organizations face both opportunities and risks with big data analytics vendors, and the risks are now profound, as data has been likened to the oil of the digital era. The growing body of research at the nexus of big data analytics and cloud computing is examined from the economic perspective, based on agency theory (AT). A conceptual framework is developed for analyzing these opportunities and challenges regarding the use of big data analytics and cloud computing in e-business environments. This framework allows organizations to engage in contracts that target competitive parity with their service-oriented decision support system (SODSS) to achieve a competitive advantage related to their core business model. A unique contribution of this paper is its perspective on how to engage a vendor contractually to achieve this competitive advantage. The framework provides insights for a manager in selecting a vendor for cloud-based big data services.

A data access framework for service-oriented rich clients

2011 ◽  
Vol 6 (2) ◽  
pp. 99-116
Author(s):  
Qi Zhao ◽  
Xuanzhe Liu ◽  
Xingrun Chen ◽  
Jiyu Huang ◽  
Gang Huang ◽  
...  
Keyword(s):  
Data Access ◽  
Service Oriented

scholarly journals Promiscuous Biological Features of Newly Emerged SARS-CoV-2 Facilitate its Unrestrained Outbreak: An Update

Coronaviruses ◽  
2021 ◽  
Vol 02 ◽  
Author(s):  
Asim Azhar ◽  
Khaled Al-hosaini ◽  
Parvez Anwar Khan ◽  
Abdul M Oanz ◽  
Qamar Zia ◽  
...  
Keyword(s):  
Life Cycle ◽  
Effective Vaccine ◽  
Preventive Strategy ◽  
Virus Structure ◽  
Positive Side ◽  
Virus Life Cycle ◽  
Prophylactic Measures ◽  
The World ◽  
Virus World ◽  
Insight Into

: The unrelenting protraction of Coronavirus Disease 2019 (COVID-19), inflicted by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), is tending to craft havoc all over the world for the past ten months. Keeping into consideration looming repercussions due to this deadly virus world over, there is an impending necessity to comprehend this newfangled contagion. To develop an effective eradication measure and preventive strategy, knowledge about the virus structure, life cycle, and metabolism is imperative. Better insight into the virus life cycle helps us to identify and design drugs that can hit crucial targets of this dreadful virus. The close genetic similarity between SARS-CoV-2 and SARS-CoV, which triggeredan outbreak in the year 2003, could be of great strategic importance in designing effective drug formulations. This will also help in leveraging immunological measures and development of leveraging immunological measures to develop an effective vaccine against SARS-CoV-2. This eventually will help us to progress our strategies to contain the virus. Not on the positive side, there is some misinformation going all around the world despite the strict regulations from the WHO and other government agencies to inform the citizens to abstain from the rumour-mongering to contain the COVID-19. Further, evidence needs to be gathered on vaccine strategies to cure the patients suffering from COVID-19. This information will also help us in designing both drug inhibitors as well as prophylactic measures against SARS-CoV-2.

scholarly journals Identification and Characterization of Human Observational Studies in Nutritional Epidemiology on Gut Microbiomics for Joint Data Analysis

Nutrients ◽  
2021 ◽  
Vol 13 (9) ◽  
pp. 3292
Author(s):  
Mariona Pinart ◽  
Katharina Nimptsch ◽  
Sofia K. Forslund ◽  
Kristina Schlicht ◽  
Miguel Gueimonde ◽  
...  
Keyword(s):  
Data Sharing ◽  
Gut Microbiome ◽  
Observational Studies ◽  
Data Access ◽  
Nutritional Epidemiology ◽  
Rrna Gene ◽  
Specific Information ◽  
Related Factors ◽  
Cross Sectional ◽  
Health And Disease

In any research field, data access and data integration are major challenges that even large, well-established consortia face. Although data sharing initiatives are increasing, joint data analyses on nutrition and microbiomics in health and disease are still scarce. We aimed to identify observational studies with data on nutrition and gut microbiome composition from the Intestinal Microbiomics (INTIMIC) Knowledge Platform following the findable, accessible, interoperable, and reusable (FAIR) principles. An adapted template from the European Nutritional Phenotype Assessment and Data Sharing Initiative (ENPADASI) consortium was used to collect microbiome-specific information and other related factors. In total, 23 studies (17 longitudinal and 6 cross-sectional) were identified from Italy (7), Germany (6), Netherlands (3), Spain (2), Belgium (1), and France (1) or multiple countries (3). Of these, 21 studies collected information on both dietary intake (24 h dietary recall, food frequency questionnaire (FFQ), or Food Records) and gut microbiome. All studies collected stool samples. The most often used sequencing platform was Illumina MiSeq, and the preferred hypervariable regions of the 16S rRNA gene were V3–V4 or V4. The combination of datasets will allow for sufficiently powered investigations to increase the knowledge and understanding of the relationship between food and gut microbiome in health and disease.

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