scholarly journals Biomolecule and Bioentity Interaction Databases in Systems Biology: A Comprehensive Review

Biomolecules ◽  
2021 ◽  
Vol 11 (8) ◽  
pp. 1245 ◽  
Author(s):  
Fotis A. Baltoumas ◽  
Sofia Zafeiropoulou ◽  
Evangelos Karatzas ◽  
Mikaela Koutrouli ◽  
Foteini Thanati ◽  
...  
Keyword(s):  
Systems Biology ◽  
Data Representation ◽  
Sources Of Information ◽  
End User ◽  
User Friendliness ◽  
Computational Approaches ◽  
Comprehensive Review ◽  
Technological Advances ◽  
Data Flood ◽  
General Scope

Technological advances in high-throughput techniques have resulted in tremendous growth of complex biological datasets providing evidence regarding various biomolecular interactions. To cope with this data flood, computational approaches, web services, and databases have been implemented to deal with issues such as data integration, visualization, exploration, organization, scalability, and complexity. Nevertheless, as the number of such sets increases, it is becoming more and more difficult for an end user to know what the scope and focus of each repository is and how redundant the information between them is. Several repositories have a more general scope, while others focus on specialized aspects, such as specific organisms or biological systems. Unfortunately, many of these databases are self-contained or poorly documented and maintained. For a clearer view, in this article we provide a comprehensive categorization, comparison and evaluation of such repositories for different bioentity interaction types. We discuss most of the publicly available services based on their content, sources of information, data representation methods, user-friendliness, scope and interconnectivity, and we comment on their strengths and weaknesses. We aim for this review to reach a broad readership varying from biomedical beginners to experts and serve as a reference article in the field of Network Biology.

Categorization of Information Loss During the Dissemination of Design Ideas

2018 ◽  
Author(s):  
Victoria Zhao ◽  
Conrad S. Tucker
Keyword(s):  
Engineering Design ◽  
Design Process ◽  
Information Source ◽  
Information Loss ◽  
Design Solution ◽  
Sources Of Information ◽  
Comprehensive Review ◽  
Engineering Design Process ◽  
Design Idea ◽  
Design Ideas

Information is transferred through a process consisting of an information source, a transmitter, a channel, a receiver and its destination. Unfortunately, during different stages of the engineering design process, there is a risk of a design idea or solution being incorrectly interpreted due to the nonlinearity of engineering design. I.e., there are many ways to communicate a single design idea or solution. This paper provides a comprehensive review and categorization of the possible sources of information loss at different stages of the engineering design process. Next, the authors present an approach that seeks to minimize information loss during certain stages of the engineering design process. The paper i) explores design process and dissemination methods in engineering design; ii) reviews prior work pertaining to these stages of the engineering design process and iii) proposes an information entropy metric that designers can utilize in order to quantify information loss at different stages of the engineering design process. Knowledge gained from this work will aid designers in selecting a suitable dissemination solution needed to effectively achieve a design solution.

Differences between end user innovators and embedded user innovators in diffusion channel selection: the moderating role of technological advances

2021 ◽  
Vol ahead-of-print (ahead-of-print) ◽  
Author(s):  
Xin Yu
Keyword(s):  
Channel Selection ◽  
Business Success ◽  
End User ◽  
Online Questionnaire ◽  
Diffusion Channel ◽  
Content Type ◽  
Segmented Markets ◽  
Technological Advances ◽  
Moderating Role

PurposeIn heterogeneously segmented markets, collaborating with product users in product innovation is important for business success. End user innovators and embedded user innovators differ in terms of their prior embeddedness in the target industry. The purpose of this study is twofold. First, the authors empirically compare these two types of user innovators in terms of their diffusion channel selection. Second, the authors analyze how the technological advances of their innovations affect this difference.Design/methodology/approachUsing an online questionnaire survey, this study collected a sample of 237 user-generated innovations in Japan and analyzed several hypotheses using quantitative statistical approaches.FindingsThe analysis shows that embedded user innovators are more likely than end user innovators to transfer their innovations to producers rather than peers. As the technological advances of their innovations increase, end user innovators' likelihood of transferring their innovation to producers increases more significantly than that of embedded user innovators.Originality/valueThis is the first paper to investigate the difference between end user innovators and embedded user innovators with respect to their diffusion channel selection as well as the moderating role of technological advances. The findings bring new perspectives to the domains of user–producer collaboration and technology transfer.

A Review of Knowledge Management Frameworks

2011 ◽  
pp. 120-236
Author(s):  
Brian Lehaney ◽  
Steve Clarke ◽  
Elayne Coakes ◽  
Gillian Jack
Keyword(s):  
Knowledge Management ◽  
Literature Review ◽  
Detailed Examination ◽  
Data Representation ◽  
Background Information ◽  
General Area ◽  
Organisational Structure ◽  
Comprehensive Review ◽  
Comprehensive Examination ◽  
New Knowledge

This research is concerned with developing a framework for the evaluation of an organisation’s potential to engage in knowledge management (an organisation’s ‘KM-readiness’, or KMR). To recap, Chapter 3 offered background information and empirical evidence of issues that need to be considered in organisations, Chapter 4 provided an overview of knowledge management, and Chapter 5 explored organisational structure, strategy, and culture in the context of knowledge management. Discussion thus far would not be sufficient to provide a robust and reasoned framework. This chapter is intended to accumulate some further and more focussed ideas as to what should be in a KMR framework, and to assist in the understanding of the material presented here and further on in this thesis. This chapter, therefore, provides a comprehensive review of published knowledge management frameworks that purport to address evaluation, implementation, and other connected areas. Before continuing, it is important to set this exercise in context. The review of frameworks is distinct from a review of literature in which the frameworks are presented. The latter is not intended here. For example, a review of a paper may involve a comprehensive critique, which includes exploration into the general area of research, clarification of the hypothesis, detailed examination of research methods and methodology, literature review, and comprehensive examination of data representation and quality. Such a review would consider the presentation of the paper, and it would critically reflect on the overall purpose of the paper and contribution made to new knowledge, either conceptual or practical. This review focuses solely on the frameworks presented in a paper and in particular those that may address evaluation of knowledge management in an organisation.

An Overview and Technological Background of Semantic Technologies

2021 ◽  
pp. 1-21
Author(s):  
Reinaldo Padilha França ◽  
Ana Carolina Borges Monteiro ◽  
Rangel Arthur ◽  
Yuzo Iano
Keyword(s):  
Semantic Web ◽  
Knowledge Representation ◽  
Data Representation ◽  
Current Data ◽  
The Internet ◽  
Semantic Technologies ◽  
Web Based ◽  
Web 3.0 ◽  
Technological Advances ◽  
The Web

The Semantic Web concept is an extension of the web obtained by adding semantics to the current data representation format. It is considered a network of correlating meanings. It is the result of a combination of web-based conceptions and technologies and knowledge representation. Since the internet has gone through many changes and steps in its web versions 1.0, 2.0, and Web 3.0, this last call of smart web, the concept of Web 3.0, is to be associated with the Semantic Web, since technological advances have allowed the internet to be present beyond the devices that were made exactly with the intention of receiving the connection, not limited to computers or smartphones since it has the concept of reading, writing, and execution off-screen, performed by machines. Therefore, this chapter aims to provide an updated review of Semantic Web and its technologies showing its technological origins and approaching its success relationship with a concise bibliographic background, categorizing and synthesizing the potential of technologies.

Drug discovery in the age of systems biology: the rise of computational approaches for data integration

2012 ◽  
Vol 23 (4) ◽  
pp. 609-616 ◽  
Author(s):  
Murat Iskar ◽  
Georg Zeller ◽  
Xing-Ming Zhao ◽  
Vera van Noort ◽  
Peer Bork
Keyword(s):  
Systems Biology ◽  
Drug Discovery ◽  
Data Integration ◽  
Computational Approaches

scholarly journals Integration of constraints documented in SBML, SBO, and the SBML Manual facilitates validation of biological models

2007 ◽  
Vol 4 (3) ◽  
pp. 252-263 ◽  
Author(s):  
Allyson L. Lister ◽  
Matthew Pocock ◽  
Anil Wipat
Keyword(s):  
Systems Biology ◽  
Representative Sample ◽  
Model Development ◽  
Structural Knowledge ◽  
Markup Language ◽  
Web Ontology Language ◽  
Biological Models ◽  
Computational Approaches ◽  
Ontology Language ◽  
Systems Biology Markup Language

Abstract The creation of quantitative, simulatable, Systems Biology Markup Language (SBML) models that accurately simulate the system under study is a time-intensive manual process that requires careful checking. Currently, the rules and constraints of model creation, curation, and annotation are distributed over at least three separate documents: the SBML schema document (XSD), the Systems Biology Ontology (SBO), and the “Structures and Facilities for Model Definition” document. The latter document contains the richest set of constraints on models, and yet it is not amenable to computational processing. We have developed a Web Ontology Language (OWL) knowledge base that integrates these three structure documents, and that contains a representative sample of the information contained within them. This Model Format OWL (MFO) performs both structural and constraint integration and can be reasoned over and validated. SBML Models are represented as individuals of OWL classes, resulting in a single computationally amenable resource for model checking. Knowledge that was only accessible to humans is now explicitly and directly available for computational approaches. The integration of all structural knowledge for SBML models into a single resource creates a new style of model development and checking.

The 1999 review of the Western Division of New South Wales

2001 ◽  
Vol 23 (1) ◽  
pp. 33 ◽  
Author(s):  
John Kerin
Keyword(s):  
Natural Resource Management ◽  
Social Issues ◽  
New South ◽  
New South Wales ◽  
Decision Makers ◽  
Comprehensive Review ◽  
South Wales ◽  
Technological Advances ◽  
Administrative Procedures ◽  
Western Division

A comprehensive review of the Western Division of New South Wales was carried out in 1998/99. The review addressed economic, environmental and social issues in New South Wales' rangelands. Six commissioned studies examined these issues in more detail. The recommendations of the review centred on streamlining administrative procedures, including Acts and regulations, addressing integrated natural resource management from a regional perspective by involving leaseholders and relevant stakeholders as representative of the broader community. It was seen as essential that scientific research and expertise, and technological advances in knowledge, be utilised by decision makers in coming to more coordinated land management decisions.

scholarly journals Combining heterogeneous data sources for neuroimaging based diagnosis: re-weighting and selecting what is important

2018 ◽  
Author(s):  
Michele Donini ◽  
Joao M. Monteiro ◽  
Massimiliano Pontil ◽  
Tim Hahn ◽  
Andreas J. Fallgatter ◽  
...  
Keyword(s):  
Feature Selection ◽  
Learning Algorithm ◽  
Multiple Kernel Learning ◽  
Clinical Information ◽  
Data Representation ◽  
Heterogeneous Data ◽  
Healthy Controls ◽  
Sources Of Information ◽  
Heterogeneous Data Sources ◽  
Selection Methodology

Combining neuroimaging and clinical information for diagnosis, as for example behavioral tasks and genetics characteristics, is potentially beneficial but presents challenges in terms of finding the best data representation for the different sources of information. Their simple combination usually does not provide an improvement if compared with using the best source alone. In this paper, we proposed a framework based on a recent multiple kernel learning algorithm called EasyMKL and we investigated the benefits of this approach for diagnosing two different mental health diseases. The well known Alzheimer's Disease Neuroimaging Initiative (ADNI) dataset tackling the Alzheimer Disease (AD) patients versus healthy controls classification task, and a second dataset tackling the task of classifying an heterogeneous group of depressed patients versus healthy controls. We used EasyMKL to combine a huge amount of basic kernels alongside a feature selection methodology, pursuing an optimal and sparse solution to facilitate interpretability. Our results show that the proposed approach, called EasyMKLFS, outperforms baselines (e.g. SVM and SimpleMKL), state-of-the-art random forests (RF) and feature selection (FS) methods.

scholarly journals ACTIVATING TO SUCCESS: A COMPREHENSIVE REVIEW OF IRRIGANT AGITATION DEVICES IN ENDODONTICS

2020 ◽  
pp. 36-38
Author(s):  
Snigdho Das
Keyword(s):  
Treatment Outcome ◽  
Root Canal ◽  
Complex Root ◽  
Canal System ◽  
Comprehensive Review ◽  
Successful Treatment Outcome ◽  
Technological Advances ◽  
Root Canal System ◽  
Irrigant Activation ◽  
Microbial Toxins

Removal of vital and necrotic remnants of pulp tissues, microorganisms, and microbial toxins from the root canal system is warranted for ensuing successful treatment outcome. Irrigation plays a major role in achieving the same. The last few years have seen a spurt in technological advances in various irrigant activation devices. This article meticulously reviews the various irrigant agitation systems available, which assists in complete disinfection of the complex root canal system.

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