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E-raamat: Classification Made Relevant: How Scientists Build and Use Classifications and Ontologies

(Freelance author with expertise in informatics, computer programming, and cancer biology)
  • Formaat: EPUB+DRM
  • Ilmumisaeg: 25-Jan-2022
  • Kirjastus: Academic Press Inc
  • Keel: eng
  • ISBN-13: 9780323972581
  • Formaat - EPUB+DRM
  • Hind: 130,97 €*
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  • Formaat: EPUB+DRM
  • Ilmumisaeg: 25-Jan-2022
  • Kirjastus: Academic Press Inc
  • Keel: eng
  • ISBN-13: 9780323972581

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Classification Made Relevant explains how classifications and ontologies are designed, and how they are used to analyze scientific information. It is through our description of the relationships among classes of objects that we are able to simplify knowledge and explore the ways in which individual classified objects behave. The book begins by describing the fundamentals of classification and leads up to a description of how computer scientists use object-oriented programming languages to model classifications and ontologies. Numerous examples are chosen from the Classification of Life, the Periodic Table of the Elements, and the symmetry relationships contained within the Classification Theorem of Finite Simple Groups. When these three classifications are tied together, they provide a relational hierarchy connecting all of the natural sciences. This book is intended to reach a multidisciplinary audience of students and professionals working in the data sciences, the library sciences, and all of the STEM sciences.

The chapters introduce and describe general concepts that can be understood by any intelligent reader. With each new concept, there follow practical examples selected from various scientific disciplines. In these cases, technical points and specialized vocabulary are linked to glossary items, where the item is clarified and expanded. Technical terms in the data sciences often have different meanings, depending on the reader's specific discipline. The word “ontology has so many meanings, it has become meaningless. Skeptics can google on the word “ontology to quickly confirm the inchoate status of this subject. In such cases, the glossary describes the different way the term has been used and will clarify its meaning within the book's context. For the benefit of computer scientists, the glossary contains short scripts written in Perl or Python or Ruby. Non-programmers will be spared from reading computer code, without missing out on the concepts covered in each chapter. By using the glossary links, every reader experiences a version of this book tailored to their personal needs and preferences.

    • Explains the theory and the practice of classification. Emphasizes the importance of classifications and ontologies to the modern fields of mathematics, physics, chemistry, biology, and medicine.
    • Includes numerous real-world examples demonstrating how bad construction technique can destroy the value of classifications and ontologies
    • Explains how we define and understand the relationships among the classes within a classification, and how the properties of a class are inherited by its subclasses.
    • Describes ontologies, and how they differ from classifications. Explains those conditions under which ontologies are useful.
    • Explains how statements of meaning are properly expressed as triples. Shows how triples can be specified by popular semantic languages. Explains how triplestores (large collections of triples) can be usefully linked to classifications and ontologies.
    • Demonstrates how classifications, ontologies, and triplestores are modeled by modern object-oriented languages.

    Arvustused

    "One of the ways in which human beings attempt to understand relationships among objects, beings and concepts is through the process of classification. Sometimes our classifications are simple (heavy vs light) and sometimes complex (the phylogeny of living things), but each attempt to develop a classification system represents an attempt to improve our understanding of the world around us. In this tour de force, Dr. Berman creates a unifying framework by which to understand successful (and unsuccessful) classification systems in fields ranging from mathematics to biology, showing the dependence of all successful classifications to at least implicit incorporation/acceptance of previous classifications in the mathematics physics chemistry biology chain, and without losing sight of the fact that the purpose of classification is understanding. Thus, development of classification systems both complements and frames the appropriate use of other tools, based on probabilistic and continuous mathematics, for understanding the world around us. The clear and detailed expositions that Dr. Berman provides in this book are useful to both scientists who wish to develop a deeper understanding of how concepts like that of the periodic table both encapsulate known science and guide its further development, and to non-scientists who wish to develop a better understanding of how scientists think. I highly recommend it." --Timothy J. O'Leary, MD, PhD, Adjunct Professor of Pathology, University of Maryland School of Medicine, Baltimore, MD, United States; former Chief Research and Development Officer, Department of Veterans Affairs

    About the author xiii
    Preface xv
    1 Sitting in class
    1(80)
    Section 1.1 Sorting things out
    1(3)
    Section 1.2 Things and their parts
    4(6)
    Section 1.3 Relationships, classes, and properties
    10(6)
    Section 1.4 Things that defy simple classification
    16(20)
    Section 1.5 Classifying by time
    36(45)
    Glossary
    45(28)
    References
    73(8)
    2 Classification logic
    81(32)
    Section 2.1 Classifications defined
    81(10)
    Section 2.2 The gift of inheritance
    91(1)
    Section 2.3 The gift of completeness
    92(4)
    Section 2.4 A classification is an evolving hypothesis
    96(2)
    Section 2.5 Widely held misconceptions
    98(15)
    Glossary
    104(6)
    References
    110(3)
    3 Ontologies and semantics
    113(42)
    Section 3.1 When classifications just won't do
    113(2)
    Section 3.2 Ontologies to the rescue
    115(2)
    Section 3.3 Quantum of meaning: The triple
    117(6)
    Section 3.4 Semantic languages
    123(7)
    Section 3.5 Why ontologies sometimes disappoint us
    130(5)
    Section 3.6 Best practices for ontologies
    135(20)
    Glossary
    141(11)
    References
    152(3)
    4 Coping with paradoxical or flawed classifications and ontologies
    155(48)
    Section 4.1 Problematica
    155(17)
    Section 4.2 Paradoxes
    172(5)
    Section 4.3 Linking classifications, ontologies, and triplestores
    177(3)
    Section 4.4 Saving hopeless classifications
    180(23)
    Glossary
    190(8)
    References
    198(5)
    5 The class-oriented programming paradigm
    203(48)
    Section 5.1 This
    Chapter in a nutshell
    203(2)
    Section 5.2 Objects and object-oriented programming languages
    205(4)
    Section 5.3 Classes and class-oriented programming
    209(8)
    Section 5.4 In the natural sciences, classifications are mono-parental
    217(5)
    Section 5.5 Listening to what objects tell us
    222(6)
    Section 5.6 A few software tools for traversing triplestores and classifications
    228(23)
    Glossary
    244(5)
    References
    249(2)
    6 The classification of life
    251(92)
    Section 6.1 All creatures great and small
    251(4)
    Section 6.2 Solving the species riddle
    255(5)
    Section 6.3 Wherever shall we put our viruses?
    260(10)
    Section 6.4 Using the classification of life to determine when aging first evolved
    270(8)
    Section 6.5 How inferences are drawn from the classification of life
    278(16)
    Section 6.6 How the classification of life unifies the biological sciences
    294(49)
    Glossary
    316(15)
    References
    331(12)
    7 The Periodic Table
    343(28)
    Section 7.1 Setting the Periodic Table
    343(5)
    Section 7.2 Braving the elements
    348(4)
    Section 7.3 All the matter that matters
    352(4)
    Section 7.4 Great deductions from anomalies in the Periodic Table
    356(15)
    Glossary
    367(2)
    References
    369(2)
    8 Classifying the universe
    371(50)
    Section 8.1 The role of mathematics in classification
    371(3)
    Section 8.2 Invariances are our laws
    374(14)
    Section 8.3 Fearful symmetry
    388(5)
    Section 8.4 The Classification Theorem
    393(5)
    Section 8.5 Symmetry groups rule the universe
    398(7)
    Section 8.6 Life, the universe, and everything
    405(16)
    Glossary
    410(8)
    References
    418(3)
    Index 421
    Jules Berman holds two Bachelor of Science degrees from MIT (in Mathematics and in Earth and Planetary Sciences), a PhD from Temple University, and an MD from the University of Miami. He was a graduate researcher at the Fels Cancer Research Institute (Temple University) and at the American Health Foundation in Valhalla, New York. He completed his postdoctoral studies at the US National Institutes of Health, and his residency at the George Washington University Medical Center in Washington, DC. Dr. Berman served as Chief of anatomic pathology, surgical pathology, and cytopathology at the Veterans Administration Medical Center in Baltimore, Maryland, where he held joint appointments at the University of Maryland Medical Center and at the Johns Hopkins Medical Institutions. In 1998, he transferred to the US National Institutes of Health as a Medical Officer and as the Program Director for Pathology Informatics in the Cancer Diagnosis Program at the National Cancer Institute. Dr. Berman is a past President of the Association for Pathology Informatics and is the 2011 recipient of the Associations Lifetime Achievement Award. He is a listed author of more than 200 scientific publications and has written more than a dozen books in his three areas of expertise: informatics, computer programming, and pathology. Dr. Berman is currently a freelance writer.