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Ontology Encyclopedia

Video Introduction

Postulates To Build On  
Structure To Build With 
Next Organizational Sequence
High School Example    

Wake Up!  
Noble Savage Myth 
1y-30 (old valuable)

0-0 Index
0-1 Preface
0-2 Read First
0-3 Gestalt Formation
0-4 Explain Ontology



1 Background 
2 Foundation


3 Observe
4 Analyze
5 Contrary
6 Synthesize
7 Thesisize

8 Youtube
9 Closing

Split Screen  
Video Index 

2003 2020 Donald James Johnson Sr. - email:

Ontology Research Group

National Center for Ontological Research

Ontology Encyclopedia

The website's purpose is: Organizing and Investigating the totality of Reality in search of what gives intelligent life's meaning. We are using an overview of Reality in logical and pattern order of evolution and complexity. With a personal 1 Background and 2 Foundation. Then digging down 36 levels of 3 Observe, 4 Analyze and 5 Contraries for the material and logical foundation before 6 Synthesizing and 7 Thesisizing back up the 36 levels on our material and logical foundation.
noun: ontology; plural noun: ontologies
  1. the branch of metaphysics dealing with the nature of being.
early 18th century: from modern Latin ontologia, from Greek ont- 'being' + -logy.
inˌsīkləˈpēdēə, enˌsīkləˈpēdēə/
noun: encyclopedia; plural noun: encyclopedias; noun: encyclopaedia; plural noun: encyclopaedias
  1. a book or set of books giving information on many subjects or on many aspects of one subject and typically arranged alphabetically.
mid 16th century: modern Latin, from pseudo-Greek enkuklopaideia for enkuklios paideia 'all-around education.'

Introduction Video

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Ontological Materialism Of This Encyclopedia

From a philosophical Perspective, ontological materialism is:

1) Belief that material things, such as particles, 
    chemical processes and energy, are more real,
    for example, than the human mind. The belief
    that physical and behavioral reality exist
    regardless of human observers.

2) Belief that cause/effect of physical reality can
    can predict and explain behavioral reality. 

3) But, untested thoughts may be false (like the
    vision of a flying horse.


About NCOR

The National Center for Ontological Research (NCOR) was established in Buffalo in 2005 with the goal of advancing the quality of ontological research and development and of establishing tools and measures for ontology evaluation and quality assurance. NCOR draws on the expertise of ontologists associated with the University at Buffalo and of their collaborators in scientific, commercial and government institutions throughout the world.

NCOR serves as a vehicle to coordinate, enhance, publicize, and seek funding for ontological research activities. It provides coordination, infrastructure, and independent review to organizations employing ontologies in fields such as defense and intelligence, management, healthcare and biomedical sciences.

It provides researchers working in ontology-related areas with specialized support in seeking external funding and in assembling collaborative, interdisciplinary teams both nationally and internationally. It provides consultant services for ontology projects especially in the defense and security fields and in health care and biomedical informatics. NCOR also engages in training and outreach endeavors that are designed to broaden the range of institutions and individuals accepting the goals of high quality ontology in both theory and practice.

What is Ontology?

Contemporary ontology is a partnership of multiple disciplines. On the one hand ontological research involves philosophers who are concerned to describe broad categories of entities and their most basic relationships. On the other hand ontologists are working in diverse fields of computer and information science to provide more narrowly focused classification systems in areas such as bioinformatics, engineering, or defense and security.

Ontologists have identified a wide range of theories and methods to aid the consistent representation of data and information using classifications of this sort, called ‘ontologies’. The idea, in all these cases, is that when bodies of data are annotated using well-structured ontologies, these data can be more easily retrieved, integrated and compared, and they can more easily be exploited for purposes of computer-based reasoning.

In biology and biomedicine, especially, ontologists have developed controlled vocabularies such as the Gene Ontology that are being used to describe the results of biological experiments in a consistent fashion that allows comparison of data pertaining to multiple species, diseases and biological systems. In government, administration and commerce ontologies are being used, similarly, to connect data across different departments (such as large government agencies) and to make these data accessible to standard software tools.

Ontologists study how definitions, classifications and relationships should be formulated using the tools of logic and formal semantics in order to most effectively achieve these goals. Their research provides foundations for diverse technologies in areas such as information integration, natural language processing, data annotation, and the construction of intelligent computer systems. Ontologies can also be used by human beings to codify and make explicit common understandings that support human-to-human communication and successful collaborative research across disciplinary boundaries.





The Ontology Research Group (ORG) is a central and significant part of the New York State Center of Excellence in Bioinformatics & Life Sciences. ORG researchers have many years of experience in ontology research in a variety of disciplines, ranging from the critical review and reconstruction of what people refer to as 'ontologies' and ontology-based applications in the biomedical domain, to creating and maintaining software like the Referent Tracking System, to supporting natural language processing and other applications in scientific domains.

The ORG currently has three sub-units:

  • The Ontology, Logic and Technology Unit (OLT) is engaged in foundational ontology research and content development, especially in the biomedical domain;
  • The Referent Tracking Unit (RTU) carries out applied research and software development pertaining to electronic health records and other data resources in the biomedical domain;
  • The Qualitative Spatiotemporal Reasoning Unit (QSR) is applying ontological techniques derived from qualitative spatiotemporal reasoning and the field of Geographic Information Systems in order to improve the representation of canonical anatomy, as well as the processing of X-ray, MRI, and other forms of image and signal data.

The VISION of the ORG is to assist scientific researchers, especially biomedical researchers, in providing a single, cumulative, and algorithmically processable database of information in their respective scientific domains.

The MISSION of the ORG is to realize this vision by supporting researchers in the creation and application of high-quality domain ontologies that enable efficient translational research and optimal clinical care.

The term 'ONTOLOGY' has a number of meanings.


The ORG collaborates with a number of centers, projects, departments, consortia, and industries so as to fulfill its vision and mission. Some of the collaborators can be found below.

  • National Center for Ontological Research
  • OBO Foundry Project
  • The University at Buffalo
  • RIDE
  • Industrial Collaborations

  • Google Custom Search


    ORG researchers are playing leading roles in a number of national and international ontology research consortia, and they have organized a wide variety of ontology training and dissemination events. The ORG is constantly involved in the organization and participation of workshops, conferences, colloquia, and other events, some of which can be found below.

  • Ontology Dissemination Events


    The competence, collaboration, and collegiality of the ORG Directors set the tone for a cohesive group of cutting-edge researchers.

    Werner Ceusters

    Werner CEUSTERS
    Louis GOLDBERG
    Barry SMITH


    ORG researchers actively publish, teach, and mentor in their respective areas of specialization, bringing a breadth of knowledge and experience to the group.


    Administrative matters of the ORG are handled expeditiously and competently by Sandra Smith.

    Sandra Smith

    701 Ellicott Street ~ Buffalo, New York 14203 ~ 716.898.8630 privacy policy | contact us

    Next Organizational Sequence

     Logical Investigation Sequence

    1 Observe
    2 Analyze
    3 Contrary
    4 Synthesize
    5 Thesisize
    1 Physical Reality Investigation Sequence 2 Behavioral Reality Investigation Sequence 3 Modeling Reality Investigation Sequence
    1 Postulates Of Physical Reality
    2 Cosmos (Space, Aether and Motion infinite 
       and eternal but finite density)
    3 Gravity And Cyclones/Strings
    4 Vortons/Photons
    5 Electrons/Positrons
    6 Protons and Neutrons
    7 Nucleus
    8 Atoms
    9 Electricity and Magnetism
    10 Crystals
    11 Molecules
    12 Cells - Cytology - Nerve Growth Factor
    13 The Organs - Physiology
    16 Brain And Nervous System - Autism
    15 The Body
    1 Existence - Is There Purpose?
    2 The Universe
    3 The Sun Earth Moon
    4 Evolution of Logical Awareness
    5 The Struggle To Civilize
    6 States
    7 Societies
    8 Communities
    9 Neighborhoods
    0 Homes
    1 Marriage
    2 Parenting Autism
    3 The Individual
    4 Anthropoculture
    1 States Of Being
    2 Caring Levels
    3 Emotional Levels
    4 Curiosity
    5 Communications
    6 Computers And Software
    7 Sovereignty
    8 End of Observations

    A Life Of Serving Intelligent
    Existence In A SpiritOf Truth
    And Passing It ToThe Next