Classification Made Relevant

Classification Made Relevant

How Scientists Build and Use Classifications and Ontologies

1st Edition - January 25, 2022

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  • Author: Jules J. Berman
  • Paperback ISBN: 9780323917865
  • eBook ISBN: 9780323972581

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Classification Made Relevant: How Scientists Build and Use Classifications and Ontologies explains how classifications and ontologies are designed and used to analyze scientific information. The book presents the fundamentals of classification, leading 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. The book's chapters introduce and describe general concepts that can be understood by any intelligent reader. With each new concept, they 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.

Key Features

  • Explains the theory and practice of classification, emphasizing the importance of classifications and ontologies to the modern fields of mathematics, physics, chemistry, biology and medicine
  • Includes numerous real-world examples that demonstrate 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 and explains conditions under which ontologies are useful


Upper division undergraduate students, graduate students, and researchers across a broad range of STM disciplines who need to organize and analyze information; graduate students, researchers and professionals in library science, computer and data science

Table of Contents

  • Cover image
  • Title page
  • Table of Contents
  • Copyright
  • Other books by Jules J. Berman
  • Dedication
  • About the author
  • Preface
  • 1: Sitting in class
  • Abstract
  • Section 1.1. Sorting things out
  • Section 1.2. Things and their parts
  • Section 1.3. Relationships, classes, and properties
  • Section 1.4. Things that defy simple classification
  • Section 1.5. Classifying by time
  • 2: Classification logic
  • Abstract
  • Section 2.1. Classifications defined
  • Section 2.2. The gift of inheritance
  • Section 2.3. The gift of completeness
  • Section 2.4. A classification is an evolving hypothesis
  • Section 2.5. Widely held misconceptions
  • 3: Ontologies and semantics
  • Abstract
  • Section 3.1. When classifications just won’t do
  • Section 3.2. Ontologies to the rescue
  • Section 3.3. Quantum of meaning: The triple
  • Section 3.4. Semantic languages
  • Section 3.5. Why ontologies sometimes disappoint us
  • Section 3.6. Best practices for ontologies
  • 4: Coping with paradoxical or flawed classifications and ontologies
  • Abstract
  • Section 4.1. Problematica
  • Section 4.2. Paradoxes
  • Section 4.3. Linking classifications, ontologies, and triplestores
  • Section 4.4. Saving hopeless classifications
  • 5: The class-oriented programming paradigm
  • Abstract
  • Section 5.1. This chapter in a nutshell
  • Section 5.2. Objects and object-oriented programming languages
  • Section 5.3. Classes and class-oriented programming
  • Section 5.4. In the natural sciences, classifications are mono-parental
  • Section 5.5. Listening to what objects tell us
  • Section 5.6. A few software tools for traversing triplestores and classifications
  • 6: The classification of life
  • Abstract
  • Section 6.1. All creatures great and small
  • Section 6.2. Solving the species riddle
  • Section 6.3. Wherever shall we put our viruses?
  • Section 6.4. Using the classification of life to determine when aging first evolved
  • Section 6.5. How inferences are drawn from the classification of life
  • Section 6.6. How the classification of life unifies the biological sciences
  • 7: The Periodic Table
  • Abstract
  • Section 7.1. Setting the Periodic Table
  • Section 7.2. Braving the elements
  • Section 7.3. All the matter that matters
  • Section 7.4. Great deductions from anomalies in the Periodic Table
  • 8: Classifying the universe
  • Abstract
  • Section 8.1. The role of mathematics in classification
  • Section 8.2. Invariances are our laws
  • Section 8.3. Fearful symmetry
  • Section 8.4. The Classification Theorem
  • Section 8.5. Symmetry groups rule the universe
  • Section 8.6. Life, the universe, and everything
  • Index

Product details

  • No. of pages: 444
  • Language: English
  • Copyright: © Academic Press 2022
  • Published: January 25, 2022
  • Imprint: Academic Press
  • Paperback ISBN: 9780323917865
  • eBook ISBN: 9780323972581

About the Author

Jules J. Berman

Jules J. Berman
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 Association’s 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.

Affiliations and Expertise

Freelance author with expertise in informatics, computer programming, and cancer biology

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