Data Science with Semantic Technologies

Preface xv 1 A Brief Introduction and Importance of Data Science 1 Karthika N., Sheela J. and Janet B. 1.1 What is Data Science? What Does a Data Scientist Do? 2 1.2 Why Data Science is in Demand? 2 1.3 History of Data Science 4 1.4 How Does Data Science Differ from Business Intelligence? 9 1.5 Data Science Life Cycle 11 1.6 Data Science Components 13 1.7 Why Data Science is Important 14 1.8 Current Challenges 15 1.8.1 Coordination, Collaboration, and Communication 16 1.8.2 Building Data Analytics Teams 16 1.8.3 Stakeholders vs Analytics 17 1.8.4 Driving with Data 17 1.9 Tools Used for Data Science 19 1.10 Benefits and Applications of Data Science 28 1.11 Conclusion 28 References 29 2 Exploration of Tools for Data Science 31 Qasem Abu Al-Haija 2.1 Introduction 32 2.2 Top Ten Tools for Data Science 35 2.3 Python for Data Science 35 2.3.1 Python Datatypes 36 2.3.2 Helpful Rules for Python Programming 37 2.3.3 Jupyter Notebook for IPython 37 2.3.4 Your First Python Program 38 2.4 R Language for Data Science 39 2.4.1 R Datatypes 39 2.4.2 Your First R Program 41 2.5 SQL for Data Science 44 2.6 Microsoft Excel for Data Science 48 2.6.1 Detection of Outliers in Data Sets Using Microsoft Excel 48 2.6.2 Regression Analysis in Excel Using Microsoft Excel 50 2.7 D3.JS for Data Science 57 2.8 Other Important Tools for Data Science 58 2.8.1 Apache Spark Ecosystem 58 2.8.2 MongoDB Data Store System 60 2.8.3 MATLAB Computing System 62 2.8.4 Neo4j for Graphical Database 63 2.8.5 VMWare Platform for Virtualization 65 2.9 Conclusion 66 References 68 3 Data Modeling as Emerging Problems of Data Science 71 Mahyuddin K. M. Nasution and Marischa Elveny 3.1 Introduction 72 3.2 Data 72 3.2.1 Unstructured Data 74 3.2.2 Semistructured Data 74 3.2.3 Structured Data 76 3.2.4 Hybrid (Un/Semi)-Structured Data 77 3.2.5 Big Data 78 3.3 Data Model Design 79 3.4 Data Modeling 81 3.4.1 Records-Based Data Model 81 3.4.2 Non–Record-Based Data Model 84 3.5 Polyglot Persistence Environment 87 References 88 4 Data Management as Emerging Problems of Data Science 91 Mahyuddin K. M. Nasution and Rahmad Syah 4.1 Introduction 92 4.2 Perspective and Context 92 4.2.1 Life Cycle 93 4.2.2 Use 95 4.3 Data Distribution 98 4.4 CAP Theorem 100 4.5 Polyglot Persistence 101 References 102 5 Role of Data Science in Healthcare 105 Anidha Arulanandham, A. Suresh and Senthil Kumar R. 5.1 Predictive Modeling—Disease Diagnosis and Prognosis 106 5.1.1 Supervised Machine Learning Models 107 5.1.2 Clustering Models 110 5.1.2.1 Centroid-Based Clustering Models 110 5.1.2.2 Expectation Maximization (EM) Algorithm 110 5.1.2.3 DBSCAN 111 5.1.3 Feature Engineering 111 5.2 Preventive Medicine—Genetics/Molecular Sequencing 111 5.2.1 Technologies for Sequencing 113 5.2.2 Sequence Data Analysis with BioPython 114 5.2.2.1 Sequence Data Formats 114 5.2.2.2 BioPython 117 5.3 Personalized Medicine 121 5.4 Signature Biomarkers Discovery from High Throughput Data 122 5.4.1 Methodology I — Novel Feature Selection Method with Improved Mutual Information and Fisher Score 123 5.4.1.1 Algorithm for the Novel Feature Selection Method with Improved Mutual Information and Fisher Score 124 5.4.1.2 Computing F-Score Values for the Features 125 5.4.1.3 Block Diagram for the Method-1 125 5.4.1.4 Data Set 126 5.4.1.5 Identification of Biomarkers Using the Feature Selection Technique-I 127 5.4.2 Feature Selection Methodology-II — Entropy Based Mean Score with mRMR 128 5.4.2.1 Algorithm for the Feature Selection Methodology-II 130 5.4.2.2 Introduction to mRMR Feature Selection 132 5.4.2.3 Data Sets 132 5.4.2.4 Identification of Biomarkers Using Rank Product 133 5.4.2.5 Fold Change Values 133 Conclusion 136 References 136 6 Partitioned Binary Search Trees (P(h)-BST): A Data Structure for Computer RAM 139 Pr. D.E Zegour 6.1 Introduction 140 6.2 P(h)-BST Structure 141 6.2.1 Preliminary Analysis 143 6.2.2 Terminology and Conventions 143 6.3 Maintenance Operations 143 6.3.1 Operations Inside a Class 145 6.3.2 Operations Between Classes (Outside a Class) 148 6.4 Insert and Delete Algorithms 153 6.4.1 Inserting a New Element 153 6.4.2 Deleting an Existing Element 157 6.5 P(h)-BST as a Generator of Balanced Binary Search Trees 160 6.6 Simulation Results 162 6.6.1 Data Structures and Abstract Data Types 164 6.6.2 Analyzing the Insert and Delete Process in Random Case 164 6.6.3 Analyzing the Insert Process in Ascending (Descending) Case 168 6.6.4 Comparing P(2)-BST/P(∞)-BST to Red-Black/AVL Trees 174 6.7 Conclusion 175 Acknowledgments 176 References 176 7 Security Ontologies: An Investigation of Pitfall Rate 179 Archana Patel and Narayan C. Debnath 7.1 Introduction 179 7.2 Secure Data Management in the Semantic Web 184 7.3 Security Ontologies in a Nutshell 187 7.4 InFra_OE Framework 189 7.5 Conclusion 193 References 193 8 IoT-Based Fully-Automated Fire Control System 199 Lalit Mohan Satapathy 8.1 Introduction 200 8.2 Related Works 201 8.3 Proposed Architecture 203 8.4 Major Components 205 8.4.1 Arduino UNO 205 8.4.2 Temperature Sensor 207 8.4.3 LCD Display (16X2) 208 8.4.4 Temperature Humidity Sensor (DHT11) 209 8.4.5 Moisture Sensor 210 8.4.6 CO2 Sensor 211 8.4.7 Nitric Oxide Sensor 212 8.4.8 CO Sensor (MQ-9) 212 8.4.9 Global Positioning System (GPS) 212 8.4.10 GSM Modem 213 8.4.11 Photovoltaic System 214 8.5 Hardware Interfacing 216 8.6 Software Implementation 218 8.7 Conclusion 222 References 223 9 Phrase Level-Based Sentiment Analysis Using Paired Inverted Index and Fuzzy Rule 225 Sheela J., Karthika N. and Janet B. 9.1 Introduction 226 9.2 Literature Survey 228 9.3 Methodology 233 9.3.1 Construction of Inverted Wordpair Index 234 9.3.1.1 Sentiment Analysis Design Framework 235 9.3.1.2 Sentiment Classification 236 9.3.1.3 Preprocessing of Data 237 9.3.1.4 Algorithm to Find the Score 240 9.3.1.5 Fuzzy System 240 9.3.1.6 Lexicon-Based Sentiment Analysis 241 9.3.1.7 Defuzzification 242 9.3.2 Performance Metrics 243 9.4 Conclusion 244 References 244 10 Semantic Technology Pillars: The Story So Far 247 Michael DeBellis, Jans Aasman and Archana Patel 10.1 The Road that Brought Us Here 248 10.2 What is a Semantic Pillar? 249 10.2.1 Machine Learning 249 10.2.2 The Semantic Approach 250 10.3 The Foundation Semantic Pillars: IRI’s, RDF, and RDFS 252 10.3.1 Internationalized Resource Identifier (IRI) 254 10.3.2 Resource Description Framework (RDF) 254 10.3.2.1 Alternative Technologies to RDF: Property Graphs 256 10.3.3 RDF Schema (RDFS) 257 10.4 The Semantic Upper Pillars: OWL, SWRL, SPARQL, and SHACL 259 10.4.1 The Web Ontology Language (OWL) 260 10.4.1.1 Axioms to Define Classes 262 10.4.1.2 The Open World Assumption 263 10.4.1.3 No Unique Names Assumption 263 10.4.1.4 Serialization 264 10.4.2 The Semantic Web Rule Language 264 10.4.2.1 The Limitations of Monotonic Reasoning 267 10.4.2.2 Alternatives to SWRL 267 10.4.3 SPARQL 268 10.4.3.1 The SERVICE Keyword and Linked Data 268 10.4.4 SHACL 271 10.4.4.1 The Fundamentals of SHACL 272 10.5 Conclusion 274 References 274 11 Evaluating Richness of Security Ontologies for Semantic Web 277 Ambrish Kumar Mishra, Narayan C. Debnath and Archana Patel 11.1 Introduction 277 11.2 Ontology Evaluation: State-of-the-Art 280 11.2.1 Domain-Dependent Ontology Evaluation Tools 281 11.2.2 Domain-Independent Ontology Evaluation Tools 282 11.3 Security Ontology 284 11.4 Richness of Security Ontologies 287 11.5 Conclusion 295 References 295 12 Health Data Science and Semantic Technologies 299 Haleh Ayatollahi 12.1 Health Data 300 12.2 Data Science 301 12.3 Health Data Science 301 12.4 Examples of Health Data Science Applications 304 12.5 Health Data Science Challenges 306 12.6 Health Data Science and Semantic Technologies 308 12.6.1 Natural Language Processing (NLP) 309 12.6.2 Clinical Data Sharing and Data Integration 310 12.6.3 Ontology Engineering and Quality Assurance (QA) 311 12.7 Application of Data Science for COVID-19 313 12.8 Data Challenges During COVID-19 Outbreak 314 12.9 Biomedical Data Science 315 12.10 Conclusion 316 References 317 13 Hybrid Mixed Integer Optimization Method for Document Clustering Based on Semantic Data Matrix 323 Tatiana Avdeenko and Yury Mezentsev 13.1 Introduction 324 13.2 A Method for Constructing a Semantic Matrix of Relations Between Documents and Taxonomy Concepts 327 13.3 Mathematical Statements for Clustering Problem 330 13.3.1 Mathematical Statements for PDC Clustering Problem 330 13.3.2 Mathematical Statements for CC Clustering Problem 334 13.3.3 Relations between PDC Clustering and CC Clustering 336 13.4 Heuristic Hybrid Clustering Algorithm 340 13.5 Application of a Hybrid Optimization Algorithm for Document Clustering 342 13.6 Conclusion 344 Acknowledgment 344 References 344 14 Role of Knowledge Data Science During COVID-19 Pandemic 347 Veena Kumari H. M. and D. S. Suresh 14.1 Introduction 348 14.1.1 Global Health Emergency 350 14.1.2 Timeline of the COVID-19 351 14.2 Literature Review 354 14.3 Model Discussion 356 14.3.1 COVID-19 Time Series Dataset 357 14.3.2 FBProphet Forecasting Model 358 14.3.3 Data Preprocessing 360 14.3.4 Data Visualization 360 14.4 Results and Discussions 362 14.4.1 Analysis and Forecasting: The World 362 14.4.2 Performance Metrics 371 14.4.3 Analysis and Forecasting: The Top 20 Countries 377 14.5 Conclusion 388 References 389 15 Semantic Data Science in the COVID-19 Pandemic 393 Michael DeBellis and Biswanath Dutta 15.1 Crises Often Are Catalysts for New Technologies 393 15.1.1 Definitions 394 15.1.2 Methodology 395 15.2 The Domains of COVID-19 Semantic Data Science Research 397 15.2.1 Surveys 398 15.2.2 Semantic Search 399 15.2.2.1 Enhancing the CORD-19 Dataset with Semantic Data 399 15.2.2.2 CORD-19-on-FHIR – Semantics for COVID-19 Discovery 400 15.2.2.3 Semantic Search on Amazon Web Services (AWS) 400 15.2.2.4 COVID*GRAPH 402 15.2.2.5 Network Graph Visualization of CORD-19 403 15.2.2.6 COVID-19 on the Web 404 15.2.3 Statistics 405 15.2.3.1 The Johns Hopkins COVID-19 Dashboard 405 15.2.3.2 The NY Times Dataset 406 15.2.4 Surveillance 406 15.2.4.1 An IoT Framework for Remote Patient Monitoring 406 15.2.4.2 Risk Factor Discovery 408 15.2.4.3 COVID-19 Surveillance in a Primary Care Network 408 15.2.5 Clinical Trials 409 15.2.6 Drug Repurposing 411 15.2.7 Vocabularies 414 15.2.8 Data Analysis 415 15.2.8.1 CODO 415 15.2.8.2 COVID-19 Phenotypes 416 15.2.8.3 Detection of “Fake News” 417 15.2.8.4 Ontology-Driven Weak Supervision for Clinical Entity Classification 417 15.2.9 Harmonization 418 15.3 Discussion 418 15.3.1 Privacy Issues 420 15.3.2 Domains that May Currently be Under Utilized 421 15.3.2.1 Detection of Fake News 421 15.3.2.2 Harmonization 421 15.3.3 Machine Learning and Semantic Technology: Synergy Not Competition 422 15.3.4 Conclusion 423 Acknowledgment 423 References 423 Index 427