Ontology: Not Just for Ontology: Not Just for Philosophers Philosophers

Anymore Anymore 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.

Three Parts To Talk:

I: Meanings of ‘Ontology’

II: Basic Formal Ontology (BFO)

III: The Vision and Mission ofthe Ontology Research

Group (ORG)

Part I:Meanings of ‘Ontology’

(1) Philosophical Ontology“I can fit wholesale evolution and a creating god into my ontology without contradiction.”“Just because it has mental existence doesn’t mean it has ontological existence.”

(2) Domain Ontology“I’m 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.”

(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.

PORPHYRIAN TREE

THING

IMMATERIAL SUBSTANCE

MATERIAL SUBSTANCE

ANIMATE (Living) ENTITY

NON-ANIMATE ENTITY

LIVING ENTITY WITH

SENSATION (ANIMAL)

LIVING ENTITY W/ OUT

SENSATION (VEGETATION)

RATIONAL ANIMAL

NON-RATIONAL ANIMAL

HUMAN

E.G., Plato Aristotle

Dr. Sucheston Dr. Arp

Cf. Linnean Taxonomy and

The Periodic Table

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.

Different Schools / Approachesto Philosophical Ontology

• We can’t know reality because we can’t 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)

(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.

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_Ontologies.pdf

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_Ontologies.pdf

Informatics:The science of information collection, categorization, management, storage, processing, retrieval, and dissemination.(Arp’s rendition)

Bioinformatics:“A 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.

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.

Example Ontology

BORROWED FROM: http://www.bio.davidson.edu/courses/genomics/2006/martens... 3DN

A Gene Ontology Example

Genetics Diseases

Ecology

Evolution Primatology

Cardiology

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 errorRESULT:- More DOMAINS that are non-interoperable, non-communicative, isolated, insolated , encapsulated “silos” of information- Lost at sea? In the sea?

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)

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 arelegion examples of IT to be found.

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”

IT: Circular Definitions

FROM GO and BRIDG

(1) Hemolysis of red blood cells=Def. “The processes by which anorganism effects hemolysis”

Cf. Filtration of kidneys=Def. “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”

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 Plato’s Euthyphro.

“Holiness is what I’m doing in prosecuting my father…”

At least one reason why we need Philosophers?

IT: Use-Mention ConfusionFROM BIRN, MeSH, NCIT, and HL7

(1)Mouse =Def. “Name for the species Mus musculus”(2)“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 ”

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”

Lost at SeaLost in the Sea

Domain Ontology e.g., genetics

Domain Ontology diseases

Domain Ontology ecology

Domain Ontology evolution

Domain Ontology primatology

Domain Ontology cardiology

(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.

(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).

(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.

(3) Formal Ontology… Salvation

EXAMPLES:(a) SUOStandard Upper Ontology

(b) DOLCEDescriptive Ontology for Linguistic and Cognitive Engineering

(c) BFOBasic Formal Ontology

Formal Ontology is like a “backbone” or “spine” making communication, interoperability, and optimal

dissemination of information possible between and among domain ontologies.

Domain Ontology e.g., genetics

Domain Ontology diseases

Domain Ontology ecology

Domain Ontology evolution

Domain Ontology primatology

Domain Ontology cardiology

Domain Ontology

e.g., genetics Domain Ontology

diseases Domain Ontology

ecology Domain Ontology

evolution Domain Ontology

primatology Domain Ontology

cardiology

Formal Ontology e.g., BFO

From This

To This

Domain Ontology

e.g., genetics Domain Ontology

diseases Domain Ontology

ecology Domain Ontology

evolution Domain Ontology

primatology Domain Ontology

cardiology

Formal Ontology e.g., BFO

RESULT:No longer lost at sea or lost in the sea

of information, biomedical or otherwise.

Part II:Basic Formal

Ontology (BFO)

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

REALISM-BASED ONTOLOGY

(a) 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)

SNAP

Continuant

Independent

Continuant

Spatial

Region

Dependent

Continuant

Generically

Dependent

Continuant

Specifically

Dependent

Continuant

Object

Object

Boundary

Object

Aggregate

Fiat Object

Part

Site

Zero

Dimensional

Region

One

Dimensional

Region

Two

Dimensional

Region

Three

Dimensional

Region

Realizable

Entity

Disposition

Function

Role

Quality

Universal: SNAP Relation: is_a

SNAP

Continuant

Independent

Continuant

Spatial

Region

Dependent

Continuant

Generically

Dependent

Continuant

Specifically

Dependent

Continuant

Object

Object

Boundary

Object

Aggregate

Fiat Object

Part

Site

Zero

Dimensional

Region

One

Dimensional

Region

Two

Dimensional

Region

Three

Dimensional

Region

Realizable

Entity

Disposition

Function

Role

Quality

Example:

Pumps Blood

Human Heart

Surface of the Heart

All Hearts in This Room

A Biopsy of the Heart

Chest Cavity

Stops if No Circulation

Pink, Smooth

SPAN

Occurrent

Processual

Entity

Temporal

Region

Spatiotemporal

Region

Scattered

Spatiotemporal

Region

Connected

Spatiotemporal

Region

Process

Process

Boundary

Process

Aggregate

Fiat Process

Part

Processual

Context

Scattered

Temporal

Region

Connected

Temporal

Region

Temporal

Instant

Temporal

Interval

Spatiotemporal

Instant

Spatiotemporal

Interval

Universal: SPAN Relation: is_a

SPAN

Occurrent

Processual

Entity

Temporal

Region

Spatiotemporal

Region

Scattered

Spatiotemporal

Region

Connected

Spatiotemporal

Region

Process

Process

Boundary

Process

Aggregate

Fiat Process

Part

Processual

Context

Scattered

Temporal

Region

Connected

Temporal

Region

Temporal

Instant

Temporal

Interval

Spatiotemporal

Instant

Spatiotemporal

Interval

Example:

ECG (EKG) Test

S/T ECG Began

S/T Region of ECG

Start/End of ECG

All ECGs in Clinic

2nd Lead Attached

Test Context

Time Occupied

Moment ECG Began

BFO RESOURCESIFOMIS BFO Website:httpp://www.ifomis.uni-saarland.de/bfo/

Barry Smith’s Website:http://ontology.buffalo.edu/smith/

Barry Smith’s Articles:e.g., http://ontology.buffalo.edu/smith/articles/SNAP_SPAN.pdf

CONCRETE STEPS:(1)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 coherenceb) compatibility with other relevant ontologiesc) human intelligibility

(5) Formalize in a computer tractable language

(6) Implement in some specific computing context

A LOT OF THIS ACTUALLY HAPPENS AT MEETINGS…

Cognizance of Informatics ProblemsCooperation of Researchers, Doctors…Conferences, Colloquia, Meetings…Clarity of Terms and RelationsCogency: Counter-Example Free?Coherency of Domain OntologiesCoordination of Domain OntologiesComputational TractabilityCommunicability of InformationCoding of Information CorrectlyConvenience of Accessibility to InformationCare of Humans/Animals (First, Do No Harm)Comfort of Humans/Animals

The Countless

Cs of Computational Categorization:

FromCognizance

ToCoordination

ToComfort

COORDINATION OF DOMAIN ONTOLOGIES

Part III:The Vision and Mission of the

Ontology Research Group (ORG)

THE ONTOLOGY RESEARCH GROUP (ORG): www.org.buffalo.edu

The 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.

(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.

(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.

ORG

OLT RTU QSR

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.

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/Presentations.html

COORDINATION OF DOMAIN ONTOLOGIES

...AS WELL AS PROFFERING OF BFO

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/areas_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.html

Sigmund Software http://www.sigmundsoftware.com/

Thank YouRobert 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.