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)
(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.
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.
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
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.
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
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.