Enabling Knowledge Creation and Sharing on the Web

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Ontology Not Just for Philosophers Anymore
Robert Arp, Ph.D. - The Ontology Research Group
(ORG) www.org.buffalo.edu - The National Center
for Biomedical Ontology (NCBO) www.bioontology.or
g Special thanks to Barry Smith and Werner
Ceusters for comments and material from articles,
books, and presentations. This work was funded
by the National Institutes of Health through the
NIH Roadmap for Biomedical Research, Grant 1 U 54
HG004028. Information on the National Centers for
Biomedical Computing can be found at
http//nihroadmap.nih.gov/bioinformatics.
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Three Parts To Talk I Meanings of
Ontology II Basic Formal Ontology
(BFO) III The Vision and Mission of the
Ontology Research Group (ORG)
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Part IMeanings of Ontology
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(1) Philosophical Ontology I can fit wholesale
evolution and a creating god into my ontology
without contradiction. Just because it has
mental existence doesnt mean it has ontological
existence. (2) Domain Ontology Im working on
an ontology for annelids. The Gene Ontology has
data on that HOX gene. (3) Formal
Ontology This upper level ontology should help
organize these domains. IEEE just came out with
the latest version of SUO that may solve some of
these problems.
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• (1) Philosophical Ontology
• Ontos (being, existence) Logos (word, account,
  explanation)
• The study of what is, of the kinds and
  structures of objects, properties, events,
  processes, and relations in every area of
  reality.
• Theoretical discipline concerned with
  accurately describing the taxonomy of all things
  that exist according to underlying entities and
  principles that make things
• A) BE what they are.
• B) BE KNOWN AS what they are.
• Synonymous with classical Metaphysics.

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PORPHYRIAN TREE
Cf. Linnean Taxonomy and The Periodic Table
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To a certain extent, all of us are Philosophical
Ontologists in that we naturally and
automatically categorize any and all things in
reality so as to understand, explain, control,
dominate, and navigate reality.
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• Different Schools / Approaches
• to Philosophical Ontology
• We cant know reality because we cant get
  beyond our sensations, perceptions, and/or ideas
  of reality (Idealism)
• We can only know the theories, languages,
  concepts, or systems of beliefs about reality,
  and reality is what minds make it (Antirealism)
• We can know reality out there as a world
  beyond our minds, and reality, ultimately, is in
  no way (e)affected by our minds (Realism)
• Reality is one kind of thing all mind (Mental
  Monism)
• Reality is one kind of thing all matter
  (Material Monism)
• Reality is two kinds of things mind and matter
  (Dualism)
• Only the Bible accurately depicts reality
  (Fundamentalism)
• Only science accurately depicts reality
  (Scientism)

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• (2) Domain Ontology
• Representation of the entities and relations
  existing within a particular domain of reality
  such as medicine, geography, ecology, or law,
  e.g., GO, FMA, EnvO.
• Opposed to ontology in the philosophical sense,
  which has all of reality as its subject matter.
• Ideally, provides a controlled, structured
  vocabulary to annotate data in order to make it
  more easily searchable by human beings and
  processable by computers.
• Synonymous (for some) with Reference Ontology.
• Task or Application Ontology runs, uses,
  exploits a domain ontology.

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AN ONTOLOGY (Ontology Research Group) a
representational artifact, comprising a taxonomy
as its main part, whose representational units
are intended to designate some combination of
universals, defined classes, and certain
relations between them. E.G.,The Gene
Ontology (GO)The Foundational Model of Anatomy
Ontology (FMA)The Environment Ontology (EnvO)
Smith et al., Towards a Reference Terminology
for Ontology Research and Development in the
Biomedical Domain, Proc KRMed 2006
http//ontology.buffalo.edu/bfo/Terminology_for_On
tologies.pdf
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A REALISM-BASED ONTOLOGY is built out of
representational units which are intended to
refer exclusively to (real) universals, and
corresponds to that part of the content of a
scientific theory that is captured by its
constituent general terms and the interrelations
between the universals denoted by these terms.
(again, ORG definition) Contrasted with-
Idealism-Based Ontology- Antirealism-Based
Ontology Smith et al., Towards a Reference
Terminology for Ontology Research and Development
in the Biomedical Domain, Proc KRMed 2006
http//ontology.buffalo.edu/bfo/Terminology_for_On
tologies.pdf
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InformaticsThe science of information
collection, categorization, management, storage,
processing, retrieval, and dissemination.(Arps
rendition)
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BioinformaticsA discipline of quantitative
analysis of information relating to biological
macro-molecules with the aid of computers.Jin
Xiong, Essential Bioinformatics (Cambridge
University Press, 2006), 3. developed in the
space occupied with mathematical and
computational biology, biometry and
biostatistics, computer science, cybernetics,
molecular evolution, genomics and proteomics,
genetics, and molecular and cell
biology.Polanski and Kimmel, Bioinformatics
(Verlag Springer, 2007), 2-3.
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Domain ontology is contrasted with- Database
stores data of ontology or whatever info.-
Rule-based Language (e.g., XSD) tells you how to
store, control, and describe an ontology or
whatever info.- Thesaurus taxonomy coupled with
relations- Taxonomy terms and glosses organized
into subsumed hierarchical relations- Glossary
catalogue of glosses (translations) in a
language- Catalogue set of terms with
meanings- Inventory checklist of items, terms,
entities- Axiomatic Theory formal system with
clear rules and semantics However, it is
arguable that an Ontology can be characterized as
a hybrid of a Taxonomy and an Axiomatic Theory.
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Example Ontology
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BORROWED FROM http//www.bio.davidson.edu/courses
/genomics/2006/martens... 3DN
A Gene Ontology Example
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• The Information Age A Sea of Information
• Varying perspectives, methodologies, ideas, and
  DATA
• More information than humans can handle
• Extraordinary depth, magnitude, and CHAOS
• Plenty of human error
• RESULT
• More DOMAINS that are non-interoperable,
  non-communicative, isolated, insolated ,
  encapsulated silos of information
• Lost at sea? In the sea?

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• Informatics Problems that Contribute to Being
  Lost at Sea
• - Dumb Beast
• - Nonsense-In-Nonsense-Out
• - Computer Solipsism
• - Human Idiosyncrasy
• Tower of Babel
• Pressures from Insurance Companies
• Legal Pressures
• - Human Error Incorrect Thinking (IT)

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IT Simply Getting the Facts Wrong FROM GO,
SNOMED, BRIDG, and UMLS (1) extracellular
region is_a cellular component (2) extrinsic
to membrane part_of membrane (3) derives
from confused with develops from (4) both
testes is_a testis (5) Animal Def. A
non-person living entity (6) An ontology is
the same thing as a database (7) An ontology
is just a taxonomy N.B. It may be the case
that the examples of IT used in this presentation
have been resolved. No matter, (sadly) there
are legion examples of IT to be found.
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IT Lack of Clear and Coherent DefinitionsFROM
NCIT, BRIDG, and SNOMED(1) Try and Define
Cancer, Gene, Neuropathy, Disease, Infectious
Disease, Bios Itself... admittedly
difficult.(2) Disease Progression Def. Cancer
that continues to grow and spread, and
Increase in size of tumor, and The worsening
of a disease over time(3) Person Def. Human
being(4) European is_a ethnic group(5)
Other European in New Zealand is_a ethnic
group(6) Mixed ethnic census group is_a
ethnic group

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IT Circular DefinitionsFROM GO and BRIDG(1)
Hemolysis of red blood cellsDef. The processes
by which anorganism effects hemolysisCf.
Filtration of kidneysDef. The processes by
which anorganism effects filtration (of
kidneys) (2) Ingredient Def. A substance
that acts as an ingredient within a product.
Note that ingredients may also have ingredients.
(3) Protection from natural killer cell
mediated cytolysis Def. The process of
protecting a cell from cytolysis by natural
killer cells
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IT Examples Instead of Definitions FROM
BRIDG(1) Adverse Event Def. (a) toxic
reaction(b) untoward occurrence in a subject
administered a pharmaceutical product(c) An
unfavorable and unintendedreaction, symptom,
syndrome, or disease encountered by a subject on
a clinical trial(2) Defeasibility Def. a
line of communication that is terminated,
boundaries for software
Basic Mistakes in Definitions 101 See Platos
Euthyphro. Holiness is what Im doing in
prosecuting my father At least one reason why
we need Philosophers?
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• IT Use-Mention Confusion
• FROM BIRN, MeSH, NCIT, and HL7
• Mouse Def. Name for the species Mus musculus
• National Socialism is_a MeSH Descriptor
• (3) Conceptual Entities Def. An organizational
  header for concepts representing mostly
  abstract entities
• (4) Animal Def. a subtype of Living Subject
  representing any animal-of-interest to the
  Personnel Management domain
• (5) living subject is_a code system

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IT Conception/Perception vs. Reality
Confusion FROM NCIT and UMLS (1) Living subject
Def. An object representing an organism (2)
Class performed activity Def. The description
of applying, dispensing or giving agents or
medications to subjects (3) Adverse Event Def.
An observation of a change in the state of a
subject that is assessed as being untoward (4)
Objective Result Def. An act of monitoring,
recognizing and noting reproducible
measurement (5) Individual allele is_a act
of observation (6) Cancer documentation is_a
cancer (7) Bacterium causes experimental model
of disease
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Lost at Sea Lost in the Sea
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(3) Formal Ontology Salvation - A discipline
which assists in making communication between and
among domain ontologies possible by providing a
common language and common formal framework for
reasoning. The fundamental role of an ontology
is to support knowledge sharing and reuse.J.
Domingue and E. Motta, "A knowledge-based news
server supporting ontology-driven story
enrichment and knowledge retrieval," in Knowledge
Acquisition, Modeling and Management 11th
European Workshop, EKAW 99 Proceedings, ed. D.
Fensel and R. Studer (Berlin Springer, 1999),
104.
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(3) Formal Ontology Salvation - Concerns, at
least (a) adoption of a set of basic
categories of objects (b) discerning what kinds
of entities fall within each of these categories
of objects(c) determining what relationships
hold within and amongst the different categories
in the domain ontology. - Relies on
philosophical ontology (thus, people like Smith,
Ceusters, Goldberg, Arp and others in the
Ontology Research Group doing this work).
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(3) Formal Ontology Salvation - Synonymous
(for some) with upper level, higher-level,
top-level, backbone, general, generic,
ontology. - Applied in bioinformatics,
intelligence analysis, management science, and in
other scientific and business fields, where it
serves as a basis for the improvement of
classification, information organization, and
automatic reasoning helping to navigate the sea
of information.
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(3) Formal Ontology Salvation EXAMPLES(a)
SUOStandard Upper Ontology (b)
DOLCEDescriptive Ontology for Linguistic and
Cognitive Engineering (c) BFOBasic Formal
Ontology
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Formal Ontology is like a backbone or spine
making communication, interoperability, and
optimal dissemination of information possible
between and among domain ontologies.
From This To This
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RESULT No longer lost at sea or lost in the
sea of information, biomedical or otherwise.
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Part IIBasic Formal Ontology (BFO)
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• BFO How Does It Work?
• General Preliminaries
• Formal applicable to all domains of
  objects...
• Barry Smith and David Woodruff Smith, The
  Cambridge Companion to Husserl, ed. Barry Smith
  and David Woodruff Smith (Cambridge Cambridge
  University Press, 1995), 28.
• Relevancy
• Perspectivalism
• Granularity
• Fallibility

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• REALISM-BASED ONTOLOGY
• Universals
• (1) Real Things or Continuants
• SNAP shots of reality
• (2) Real Processes or Occurrents
• SPAN of time
• (b) Relations
• (which are also universals of a different type)

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Universal SNAP
Relation is_a
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Example
Human Heart
Surface of the Heart
Pink, Smooth
All Hearts in This Room
Stops if No Circulation
A Biopsy of the Heart
Pumps Blood
Chest Cavity
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Universal SPAN
Relation is_a
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Example
ECG (EKG) Test
Start/End of ECG
S/T ECG Began
Moment ECG Began
All ECGs in Clinic
S/T Region of ECG
Time Occupied
2nd Lead Attached
Test Context
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BFO RESOURCESIFOMIS BFO Websitehttpp//www.ifom
is.uni-saarland.de/bfo/Barry Smiths
Websitehttp//ontology.buffalo.edu/smith/
Barry Smiths Articlese.g.,
http//ontology.buffalo.edu/smith/articles/SNAP_S
PAN.pdf
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• CONCRETE STEPS
• Explicitly demarcate the entities of domain
  ontology
• (2) Determine the universals and relations in
  domain
• (3) Concretize information in a representational
  artifact
• (4) Regiment the information to ensure
• a) logical, philosophical, and scientific
  coherence
• b) compatibility with other relevant ontologies
• c) human intelligibility
• (5) Formalize in a computer tractable language
• (6) Implement in some specific computing context
• A LOT OF THIS ACTUALLY HAPPENS AT MEETINGS

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Cognizance of Informatics Problems Cooperation of
Researchers, Doctors Conferences, Colloquia,
Meetings Clarity of Terms and Relations Cogency
Counter-Example Free? Coherency of Domain
Ontologies Coordination of Domain
Ontologies Computational Tractability Communicabil
ity of Information Coding of Information
Correctly Convenience of Accessibility to
Information Care of Humans/Animals (First, Do No
Harm) Comfort of Humans/Animals
The Countless Cs of Computational
Categorization From Cognizance To Coordination T
o Comfort
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COORDINATION OF DOMAIN ONTOLOGIES
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Part IIIThe Vision and Mission of the Ontology
Research Group (ORG)
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THE ONTOLOGY RESEARCH GROUP (ORG)
www.org.buffalo.eduThe ORG currently has three
sub-units(1) The Ontology, Logic and
Technology Unit (OLT) is engaged in foundational
ontology research and content development,
especially in the biomedical domain.
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(2) 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.
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(3) 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.
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ORGOLT RTU QSR
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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.
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CONCRETELY, THIS MEANS - 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 all around the
world. See http//org.buffalo.edu/rarp/Presenta
tions.html
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...AS WELL AS PROFFERING OF BFO
COORDINATION OF DOMAIN ONTOLOGIES
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A Few ORG Collaborators - NCBO
http//bioontology.org/- NCOR http//ncor.us/-
ECOR http//www.ecor.uni-saarland.de/home.html -
OBO Foundry Project http//obofoundry.org/- UB
http//philosophy.buffalo.edu/contrib/graduate/are
as_of_study/phd.shtml - IFOMIS
http//www.ifomis.uni-saarland.de/ - RIDE
http//www.srdc.metu.edu.tr/webpage/projects/ride/
- Industrial Collaborations Medtuity, Inc.
http//www.org.buffalo.edu/RTU/indcollabs.htmlSig
mund Software http//www.sigmundsoftware.com/
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Thank You Robert Arp, Ph.D. - The Ontology
Research Group (ORG) www.org.buffalo.edu - The
National Center for Biomedical Ontology
(NCBO) www.bioontology.org Special thanks to
Barry Smith and Werner Ceusters for comments and
material from articles, books, and
presentations. This work was funded by the
National Institutes of Health through the NIH
Roadmap for Biomedical Research, Grant 1 U 54
HG004028. Information on the National Centers for
Biomedical Computing can be found at
http//nihroadmap.nih.gov/bioinformatics.