Semantic Breakthrough in Drug Discovery
Semantic Breakthrough in Drug Discovery

Author: Bin Chen

Publisher: Springer Nature

Published: 2022-06-01

Total Pages: 10

ISBN-13: 3031794567

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The current drug development paradigm---sometimes expressed as, ``One disease, one target, one drug''---is under question, as relatively few drugs have reached the market in the last two decades. Meanwhile, the research focus of drug discovery is being placed on the study of drug action on biological systems as a whole, rather than on individual components of such systems. The vast amount of biological information about genes and proteins and their modulation by small molecules is pushing drug discovery to its next critical steps, involving the integration of chemical knowledge with these biological databases. Systematic integration of these heterogeneous datasets and the provision of algorithms to mine the integrated datasets would enable investigation of the complex mechanisms of drug action; however, traditional approaches face challenges in the representation and integration of multi-scale datasets, and in the discovery of underlying knowledge in the integrated datasets. The Semantic Web, envisioned to enable machines to understand and respond to complex human requests and to retrieve relevant, yet distributed, data, has the potential to trigger system-level chemical-biological innovations. Chem2Bio2RDF is presented as an example of utilizing Semantic Web technologies to enable intelligent analyses for drug discovery.Table of Contents: Introduction / Data Representation and Integration Using RDF / Data Representation and Integration Using OWL / Finding Complex Biological Relationships in PubMed Articles using Bio-LDA / Integrated Semantic Approach for Systems Chemical Biology Knowledge Discovery / Semantic Link Association Prediction / Conclusions / References / Authors' Biographies

Semantic Breakthrough in Drug Discovery
Semantic Breakthrough in Drug Discovery

Author: Bin Chen

Publisher: Morgan & Claypool Publishers

Published: 2014-10-01

Total Pages: 144

ISBN-13: 1627054510

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The current drug development paradigm---sometimes expressed as, ``One disease, one target, one drug''---is under question, as relatively few drugs have reached the market in the last two decades. Meanwhile, the research focus of drug discovery is being placed on the study of drug action on biological systems as a whole, rather than on individual components of such systems. The vast amount of biological information about genes and proteins and their modulation by small molecules is pushing drug discovery to its next critical steps, involving the integration of chemical knowledge with these biological databases. Systematic integration of these heterogeneous datasets and the provision of algorithms to mine the integrated datasets would enable investigation of the complex mechanisms of drug action; however, traditional approaches face challenges in the representation and integration of multi-scale datasets, and in the discovery of underlying knowledge in the integrated datasets. The Semantic Web, envisioned to enable machines to understand and respond to complex human requests and to retrieve relevant, yet distributed, data, has the potential to trigger system-level chemical-biological innovations. Chem2Bio2RDF is presented as an example of utilizing Semantic Web technologies to enable intelligent analyses for drug discovery. Table of Contents: Introduction / Data Representation and Integration Using RDF / Data Representation and Integration Using OWL / Finding Complex Biological Relationships in PubMed Articles using Bio-LDA / Integrated Semantic Approach for Systems Chemical Biology Knowledge Discovery / Semantic Link Association Prediction / Conclusions / References / Authors' Biographies

Semantic Mining of Social Networks
Semantic Mining of Social Networks

Author: Jie Tang

Publisher: Springer Nature

Published: 2022-06-01

Total Pages: 193

ISBN-13: 3031794621

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Online social networks have already become a bridge connecting our physical daily life with the (web-based) information space. This connection produces a huge volume of data, not only about the information itself, but also about user behavior. The ubiquity of the social Web and the wealth of social data offer us unprecedented opportunities for studying the interaction patterns among users so as to understand the dynamic mechanisms underlying different networks, something that was previously difficult to explore due to the lack of available data. In this book, we present the architecture of the research for social network mining, from a microscopic point of view. We focus on investigating several key issues in social networks. Specifically, we begin with analytics of social interactions between users. The first kinds of questions we try to answer are: What are the fundamental factors that form the different categories of social ties? How have reciprocal relationships been developed from parasocial relationships? How do connected users further form groups? Another theme addressed in this book is the study of social influence. Social influence occurs when one's opinions, emotions, or behaviors are affected by others, intentionally or unintentionally. Considerable research has been conducted to verify the existence of social influence in various networks. However, few literature studies address how to quantify the strength of influence between users from different aspects. In Chapter 4 and in [138], we have studied how to model and predict user behaviors. One fundamental problem is distinguishing the effects of different social factors such as social influence, homophily, and individual's characteristics. We introduce a probabilistic model to address this problem. Finally, we use an academic social network, ArnetMiner, as an example to demonstrate how we apply the introduced technologies for mining real social networks. In this system, we try to mine knowledge from both the informative (publication) network and the social (collaboration) network, and to understand the interaction mechanisms between the two networks. The system has been in operation since 2006 and has already attracted millions of users from more than 220 countries/regions.

Social Semantic Web Mining
Social Semantic Web Mining

Author: Tope Omitola

Publisher: Springer Nature

Published: 2022-06-01

Total Pages: 138

ISBN-13: 3031794591

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The past ten years have seen a rapid growth in the numbers of people signing up to use Web-based social networks (hundreds of millions of new members are now joining the main services each year) with a large amount of content being shared on these networks (tens of billions of content items are shared each month). With this growth in usage and data being generated, there are many opportunities to discover the knowledge that is often inherent but somewhat hidden in these networks. Web mining techniques are being used to derive this hidden knowledge. In addition, the Semantic Web, including the Linked Data initiative to connect previously disconnected datasets, is making it possible to connect data from across various social spaces through common representations and agreed upon terms for people, content items, etc. In this book, we detail some current research being carried out to semantically represent the implicit and explicit structures on the Social Web, along with the techniques being used to elicit relevant knowledge from these structures, and we present the mechanisms that can be used to intelligently mesh these semantic representations with intelligent knowledge discovery processes. We begin this book with an overview of the origins of the Web, and then show how web intelligence can be derived from a combination of web and Social Web mining. We give an overview of the Social and Semantic Webs, followed by a description of the combined Social Semantic Web (along with some of the possibilities it affords), and the various semantic representation formats for the data created in social networks and on social media sites. Provenance and provenance mining is an important aspect here, especially when data is combined from multiple services. We will expand on the subject of provenance and especially its importance in relation to social data. We will describe extensions to social semantic vocabularies specifically designed for community mining purposes (SIOCM). In the last three chapters, we describe how the combination of web intelligence and social semantic data can be used to derive knowledge from the Social Web, starting at the community level (macro), and then moving through group mining (meso) to user profile mining (micro).

Natural Language Processing for the Semantic Web
Natural Language Processing for the Semantic Web

Author: Diana Maynard

Publisher: Springer Nature

Published: 2022-05-31

Total Pages: 182

ISBN-13: 3031794745

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This book introduces core natural language processing (NLP) technologies to non-experts in an easily accessible way, as a series of building blocks that lead the user to understand key technologies, why they are required, and how to integrate them into Semantic Web applications. Natural language processing and Semantic Web technologies have different, but complementary roles in data management. Combining these two technologies enables structured and unstructured data to merge seamlessly. Semantic Web technologies aim to convert unstructured data to meaningful representations, which benefit enormously from the use of NLP technologies, thereby enabling applications such as connecting text to Linked Open Data, connecting texts to each other, semantic searching, information visualization, and modeling of user behavior in online networks. The first half of this book describes the basic NLP processing tools: tokenization, part-of-speech tagging, and morphological analysis, in addition to the main tools required for an information extraction system (named entity recognition and relation extraction) which build on these components. The second half of the book explains how Semantic Web and NLP technologies can enhance each other, for example via semantic annotation, ontology linking, and population. These chapters also discuss sentiment analysis, a key component in making sense of textual data, and the difficulties of performing NLP on social media, as well as some proposed solutions. The book finishes by investigating some applications of these tools, focusing on semantic search and visualization, modeling user behavior, and an outlook on the future.

The Epistemology of Intelligent Semantic Web Systems
The Epistemology of Intelligent Semantic Web Systems

Author: Mathieu d'Aquin

Publisher: Springer Nature

Published: 2022-05-31

Total Pages: 78

ISBN-13: 3031794710

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The Semantic Web is a young discipline, even if only in comparison to other areas of computer science. Nonetheless, it already exhibits an interesting history and evolution. This book is a reflection on this evolution, aiming to take a snapshot of where we are at this specific point in time, and also showing what might be the focus of future research. This book provides both a conceptual and practical view of this evolution, especially targeted at readers who are starting research in this area and as support material for their supervisors. From a conceptual point of view, it highlights and discusses key questions that have animated the research community: what does it mean to be a Semantic Web system and how is it different from other types of systems, such as knowledge systems or web-based information systems? From a more practical point of view, the core of the book introduces a simple conceptual framework which characterizes Intelligent Semantic Web Systems. We describe this framework, the components it includes, and give pointers to some of the approaches and technologies that might be used to implement them. We also look in detail at concrete systems falling under the category of Intelligent Semantic Web Systems, according to the proposed framework, allowing us to compare them, analyze their strengths and weaknesses, and identify the key fundamental challenges still open for researchers to tackle.

Bioinformatics and Biomedical Engineering
Bioinformatics and Biomedical Engineering

Author: Ignacio Rojas

Publisher: Springer

Published: 2018-04-19

Total Pages: 571

ISBN-13: 3319787233

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This two-volume set LNBI 10813 and LNBI 10814 constitutes the proceedings of the 6th International Work-Conference on Bioinformatics and Biomedical Engineering, IWBBIO 2018, held in Granada, Spain, in April 2018.The 88 regular papers presented were carefully reviewed and selected from 273 submissions. The scope of the conference spans the following areas: bioinformatics for healthcare and diseases; bioinformatics tools to integrate omics dataset and address biological question; challenges and advances in measurement and self-parametrization of complex biological systems; computational genomics; computational proteomics; computational systems for modelling biological processes; drug delivery system design aided by mathematical modelling and experiments; generation, management and biological insights from big data; high-throughput bioinformatic tools for medical genomics; next generation sequencing and sequence analysis; interpretable models in biomedicine and bioinformatics; little-big data. Reducing the complexity and facing uncertainty of highly underdetermined phenotype prediction problems; biomedical engineering; biomedical image analysis; biomedical signal analysis; challenges in smart and wearable sensor design for mobile health; and healthcare and diseases.

Knowledge Graphs
Knowledge Graphs

Author: Aidan Hogan

Publisher: Springer Nature

Published: 2022-06-01

Total Pages: 247

ISBN-13: 3031019180

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This book provides a comprehensive and accessible introduction to knowledge graphs, which have recently garnered notable attention from both industry and academia. Knowledge graphs are founded on the principle of applying a graph-based abstraction to data, and are now broadly deployed in scenarios that require integrating and extracting value from multiple, diverse sources of data at large scale. The book defines knowledge graphs and provides a high-level overview of how they are used. It presents and contrasts popular graph models that are commonly used to represent data as graphs, and the languages by which they can be queried before describing how the resulting data graph can be enhanced with notions of schema, identity, and context. The book discusses how ontologies and rules can be used to encode knowledge as well as how inductive techniques—based on statistics, graph analytics, machine learning, etc.—can be used to encode and extract knowledge. It covers techniques for the creation, enrichment, assessment, and refinement of knowledge graphs and surveys recent open and enterprise knowledge graphs and the industries or applications within which they have been most widely adopted. The book closes by discussing the current limitations and future directions along which knowledge graphs are likely to evolve. This book is aimed at students, researchers, and practitioners who wish to learn more about knowledge graphs and how they facilitate extracting value from diverse data at large scale. To make the book accessible for newcomers, running examples and graphical notation are used throughout. Formal definitions and extensive references are also provided for those who opt to delve more deeply into specific topics.

Web Data APIs for Knowledge Graphs
Web Data APIs for Knowledge Graphs

Author: Albert Meroño-Peñuela

Publisher: Springer Nature

Published: 2022-05-31

Total Pages: 92

ISBN-13: 3031019172

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This book describes a set of methods, architectures, and tools to extend the data pipeline at the disposal of developers when they need to publish and consume data from Knowledge Graphs (graph-structured knowledge bases that describe the entities and relations within a domain in a semantically meaningful way) using SPARQL, Web APIs, and JSON. To do so, it focuses on the paradigmatic cases of two middleware software packages, grlc and SPARQL Transformer, which automatically build and run SPARQL-based REST APIs and allow the specification of JSON schema results, respectively. The authors highlight the underlying principles behind these technologies—query management, declarative languages, new levels of indirection, abstraction layers, and separation of concerns—, explain their practical usage, and describe their penetration in research projects and industry. The book, therefore, serves a double purpose: to provide a sound and technical description of tools and methods at the disposal of publishers and developers to quickly deploy and consume Web Data APIs on top of Knowledge Graphs; and to propose an extensible and heterogeneous Knowledge Graph access infrastructure that accommodates a growing ecosystem of querying paradigms.

Entity Resolution in the Web of Data
Entity Resolution in the Web of Data

Author: Vassilis Christophides

Publisher: Springer Nature

Published: 2022-05-31

Total Pages: 106

ISBN-13: 3031794680

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In recent years, several knowledge bases have been built to enable large-scale knowledge sharing, but also an entity-centric Web search, mixing both structured data and text querying. These knowledge bases offer machine-readable descriptions of real-world entities, e.g., persons, places, published on the Web as Linked Data. However, due to the different information extraction tools and curation policies employed by knowledge bases, multiple, complementary and sometimes conflicting descriptions of the same real-world entities may be provided. Entity resolution aims to identify different descriptions that refer to the same entity appearing either within or across knowledge bases. The objective of this book is to present the new entity resolution challenges stemming from the openness of the Web of data in describing entities by an unbounded number of knowledge bases, the semantic and structural diversity of the descriptions provided across domains even for the same real-world entities, as well as the autonomy of knowledge bases in terms of adopted processes for creating and curating entity descriptions. The scale, diversity, and graph structuring of entity descriptions in the Web of data essentially challenge how two descriptions can be effectively compared for similarity, but also how resolution algorithms can efficiently avoid examining pairwise all descriptions. The book covers a wide spectrum of entity resolution issues at the Web scale, including basic concepts and data structures, main resolution tasks and workflows, as well as state-of-the-art algorithmic techniques and experimental trade-offs.