Ontology and Ontology and RadLexRadLex

Robert Arp, Ph.D.Ontology Research Group (ORG)

www.org.buffalo.eduNational Center for Biomedical Ontology

(NCBO)www.bioontology.org

This work was funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant 1 U 54 HG004028. Information on the National Centers for

Biomedical Computing can be found at http://nihroadmap.nih.gov/bioinformatics.

Problem: radiologist wondering if radiation therapy in chest is linked to Cauda Equina Syndrome in lower back.

she needs data and information to find a solution

- calls colleagues- sends emails- queries RadLex

Problem: radiologist wondering if radiation therapy in chest is linked to Cauda Equina Syndrome in lower back.

She needs data and information to find a solution

- calls colleagues- sends emails- queries RadLex

RadLex:A Lexicon for Uniform Indexing and Retrieval of Radiology Information Resources

RadLex:A Lexicon for Uniform Indexing and Retrieval of Radiology Information Resources

direct result of the information age and information science

Informatics:the science of data and information collection, categorization, management, storage, processing, retrieval, and dissemination.

Informatics:the science of data and information collection, categorization, management, storage, processing, retrieval, and dissemination.

retrieval and dissemination:the goal of information science

Informatics:the science of data and information collection, categorization, management, storage, processing, retrieval, and dissemination.

but goal depends upon accurate categorization and

management

Computers are dumb beasts:At this point,* they can mostly only accurately output what we accurately input.

* Not ruling out the possibility of human-like thinking in the future

So, a central informatics problem that hampers retrieval and dissemination is:

incorrect thinking (IT) associated with categorization and management of data and information

Can’t get the data and/or info:

- radiologist gives up the search in frustration- cure is not found- suffering is not relieved*

* moral obligation to retrieve and disseminate data and information?

To combat incorrect thinking (IT) and assist in the accurate categorization and management of data and information so that retrieval and dissemination is maximally possible:

ontologies are used

What is an ontology?

(1)Philosophical Ontology(2)Domain Ontology(3)Formal 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.”

- 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

- “The branch of Metaphysics that studies the nature of existence.” Random House College Dictionary

PORPHYRIAN TREE

Compare:Linnean Taxonomy and Periodic Table

PORPHYRIAN TREE

Compare:Linnean Taxonomy and Periodic Table

Sub-types (children) should inherit all the features of the relevant type (parent)

PORPHYRIAN TREE

Compare:Linnean Taxonomy and Periodic Table

Sub-types (children) should inherit all the features of the relevant type (parent)

A is_a B that/which CsA is_a B that/which has Cs- rational animal (A) is_a living entity with sensation (B) that has the capacity for conscious thinking (C)

Sub-types (children) should inherit all the features of the relevant type (parent) along with some differentia (distinguishing feature)

A is_a B that/which CsA is_a B that/which has Cs

- radiology (A) is_a science (B) that deals with medical imaging so as to understand, diagnose… (C)- domain ontology is_a ontology that deals with a specific area, sphere, or portion of reality

- mouse trap is_a rodent trap which captures mice

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.

What is an ontology?

(1)Philosophical Ontology(2)Domain Ontology(3)Formal Ontology

(2) Domain Ontology“...I’m working on an ontology for annelids.”

“...the Gene Ontology has data on that HOX gene.”

Representation of the entities and relations existing within a particular domain of reality such as biology, medicine, geography, ecology, or law- Gene Ontology (GO)- Foundational Model of Anatomy (FMA)- Environment Ontology (EnvO)

See http://www.obofoundry.org/

- 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

ONTOLOGY:

“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.” ** Smith, B., Kusnierczyk, W., Schober, D., & Ceusters, W. (2006). Towards a reference terminology for ontology research and development in the biomedical domain. Proceedings of KR-MED 2006, 1, 1-14.

Domain ontology contrasted with:

- Database- Rule-Based Language - Thesaurus- Glossary- Catalogue- Inventory- Axiomatic Theory- Simple Taxonomy

Ontology hybrid of:

- Taxonomy - Various Relations- Axiomatic Rules of Inference

Domain ontology contrasted with:

- Database- Rule-Based Language - Thesaurus- Glossary- Catalogue- Inventory- Axiomatic Theory- Simple Taxonomy

RadLex, as of now, is a thesaurus of terms, although confuses terms and entities those terms refer to…

Mechanism

Doorbell Ther-mometer Clock Trap

Animal Trap

Rodent Trap

Mouse Trap

Spring-Loaded Bar Mouse Trap

Electric Mouse Trap

Glue Mouse Trap

Rat Trap

Insect Trap Bear Trap Fish Trap

Human Trap

Simple Taxonomy:is_a, sub-type relation

Basic Mouse Trap Classification

mouse trapping process

mouse trappee

role

part_of preceded_by has_agent inheres_in adjacent_to

baiting of mouse trap

trapping of mouse

mouse trappee

mouse trapper

removal of mouse

s-l mouse trap

entrance of mouse

mouse trapper

role

s-l trap attraction

s-l trap function

s-l bait trigger

s-l platform

s-l spring release hook

s-l trapping bar

s-l spring

Beginnings of Mouse Trap

Domain Ontology

technician

MRI test

MRI machine

image

referral

patient

radiologist

contrast

patient’s role

machine’s function

part_of preceded_by has_participant inheres_in has_output

technician’s role

start of

test

contrast’s function

radiologist’s role

end of

test Beginnings of MRI Test Ontology

A Gene Ontology Example:

Cytokinesis

is_a ─part_of ─

A Gene Ontology Example

Part of a Scientific Experiment Ontology

Part of a Scientific Experiment Ontology

p/o = part_of

= is_a

Now, it’s fine to have all of these domain ontologies attempting to classify and categorize data and information…

But, there is so much data and information…

Crazy and overwhelming, isn’t it?

So, instead of using a STANDARD like the

Periodic Table of Elements, people start classifying

things their own different ways…

this results in…

Data

Data

Data

Data

Data Data

Data

SILO EFFECT

Data

Data

Data

Data

Data Data

Data

SILO EFFECT

PROBLEM:DE-SILOING all of this domain data and information so that it may be queried effectively,

shared, and re-used

INTEROPERABILITY

PROBLEM:DE-SILOING all of this domain data and information so that it may be queried effectively,

shared, and re-used

INTEROPERABILITY

SOLUTION:

FORMAL ONTOLOGY:

- Upper-level- Applicable to any domain

What is an ontology?

(1)Philosophical Ontology(2)Domain Ontology(3)Formal Ontology

Assists in making communication between and among domain ontologies possible by providing:

- Common language- Common formal framework for reasoning

So, just as ENGLISH is a common world language enabling different people to communicate in common

So too, FORMAL ONTOLOGY is a common “language” enabling different domain ontologies to communicate in common

Formal ontology is like a backbone or spine making communication, interoperability, and

optimal dissemination of data and information possible between and among domain

ontologies

Data

Data

Data

Data

Data

Data

Data

Formal Ontology E.G., Basic Formal Ontology

Formal ontology is like a backbone or spine making communication, interoperability, and

optimal dissemination of data and information possible between and among domain

ontologies

Data

Data

Data

Data

Data

Data

Data

Formal Ontology E.G., Basic Formal Ontology

Data

Data

Data

Data

Data

Data

Data

Formal Ontology E.G., Basic Formal Ontology

From this…

To this…

Data

Data

Data

Data

Data Data

Data

From this…

To this…

From this…

To this…

Basic Formal Ontology (BFO)

REALISM-BASED ONTOLOGYUniversals

(1) real objects, substances, endurants, or continuants- SNAP shots of reality

(2) real processes, activities,perdurants, or occurrents- SPAN of time

Relationsis_a, part_of, has_participant...

continuants vs. occurrents

In classifying parts of reality, we keep track of these two different kinds of

entities in two different ways

continuant (substance, object)

t i m

e

occurrent (process)

continuant entities- have continuous existence in time- preserve their identity through change- exist in toto, if they exist at all

occurrent entities- have temporal parts- unfold themselves phase by phase- exist only in their phases/stages

continuant entities- have continuous existence in time- preserve their identity through change- exist in toto, if they exist at all

occurrent entities- have temporal parts- unfold themselves phase by phase- exist only in their phases/stages

objects, qualities, functions

processes, activities

continuant Relation: is_a

Sub-types (children) should inherit all the features of the relevant type (parent)

continuant

human heart

surface of the heart

all hearts in this room

a biopsy of the heart

chest cavity

pink, smooth

stops if no circulation

pumps blood

prop in a display

HUMAN HEART

occurrent Relation: is_a

occurrent

ECG (EKG) test

start/end of ECG

all ECGs in clinic

2nd lead attached

activities in clinic

s/t ECG began

s/t region of ECG

moment ECG began

time occupied

ECG/EKG TESTECG/EKG TEST

(1)Philosophical Ontology(2)Domain Ontology(3)Formal Ontology

Basic principles from philosophical ontology and formal ontology can assist a domain like radiology and a domain ontology like RadLex (although, RadLex is at the beginning stages of a domain ontology)

Fundamental Step:

Clear up the incorrect thinking

(IT) in Radlex

Incorrect Thinking (IT):- simply getting the facts wrong- perception/reality confusions- using examples instead of definitions when defining something- circular definitions- equivocation of terms- use/mention confusions- unclear or incoherent definitions

Incorrect Thinking (IT):

- these are just a few…- many more problems…- problems are legion in databases

- we’ll look at just a few problems in RadLex

IT: simply getting the facts wrong:True, these are all terms, but the terms are supposed to be referring to the actual entities in reality; confusing classification of terms with a taxonomy of things

IT: simply getting the facts wrong:Is a substance a subtype of term?Is an imaging procedure attribute a sub-type of term?None of these are terms, they are things.

IT: unclear or incoherent definitions:imaging procedure attribute(a)is not really a child/sub-type of RadLex term and(b) it is the only child when, on this account, treatment, substance, etc., should be subtypes as well

IT: use/mention confusion:At the same time these terms are being used as a taxonomy that refers to reality, and mentioned in a lexical classification. Terms are representations that refer to things, but are being treated as the things themselves… confusion!

Where is the definition of a RadLex term?Where are some examples?How am I supposed to know what these things are?

?

Is a biopsy an imaging purpose?Is an infusion a purpose?Is an imaging purpose an imaging procedure attribute?Where are the definitions?

Is a biopsy a RadLex term?Is an infusion a RadLex term?

Sub-types (children) should inherit all the features of the relevant type (parent)

IT: using examples instead of definitions when defining something

- I still don’t know what an imaging service request is.- Also, isn’t a request something different from exams?- I know what an example of it might be…

Also, isn’t a request something different from an exam or exams?

Compare:Drinking service request

Def.=The drinks that can be ordered by patrons at a bar A synonym is a

RadLex child, too?

A foreign body is a child of finding?

A missile, by definition, is a foreign body?I can see it playing a role as a foreign body, but its essence is to be a foreign body?

Same with personal item, surgical implement, and others…

Three Levels to Keep Straight

Level 1: The entities in reality such as universals and relations

Level 2: Cognitive representations of this reality on the part of scientists

Level 3: Publicly accessible concretizations of these cognitive representations in textual, graphical, or computational representational artifacts (like RadLex composed of terms)

Cognitive representationsRepresentational artifacts

Reality

Three Levels to Keep Straight

- Bertaud, V., Belhadj, I., Dameron, O., Garcelon, N., Hendaoui, L., Marin, F., & Duvauferrier, R. (2007). Computerizing the radiological sign. Journal of Radiology, 88, 27-37.- Fielding, J., & Marwede, D. (2006). Four ontological models for radiological diagnostics. Studies in Health Technology and Informatics, 124, 761-766.- Kahn, C., Channin, D., & Rubin, D. (2006). An ontology for PACS integration. Journal of Digital Imaging, 19, 316-327.- Marwede, D., & Fielding, M. (2005). The epistemological-ontological divide in clinical radiology. Studies in Health Technology and Informatics, 116, 749-754.- Pommert, A., Höhne, K., Pflesser, B., Richter, E., Riemer, M., Schiemann, T., Schubert, R., Schumacher, U., & Tiede, U. (2001). Creating a high-resolution spatial/symbolic model of the inner organs based on the visible human. Medical Image Analysis, 5, 221-228.- Rubin, D. (2007). Creating and curating a terminology for radiology: Ontology modeling and analysis. Journal of Digital Imaging. Available at: http://www.springerlink.com/content/ 978708n776738132/fulltext.pdf.- Rubin, D., Dameron, O., Bashir, Y., Grossman, D., Dev, P., & Musen, M. (2006). Using ontologies linked with geometric models to reason about penetrating injuries. Artificial Intelligence in Medicine, 37, 167-176.

Radiology and Ontology Literature

Arp, R., Romagnoli, C., Chhem, R., & Overton, J. (2008).

Radiological and Biomedical Knowledge Integration: The Ontological Way.

In R. Chhem, K. Hibbert, & T. Van Deven (Eds.), Radiology Education (Chapter 8, pp. 87-104). Berlin: Springer-Verlag.

• Baxevanis, A., & Ouellette, B. (2005). Bioinformatics: A practical guide to the analysis of genes and proteins. Hoboken, NJ: Wiley.

• Berman, J. (2006). Biomedical informatics. London: Jones & Bartlett Publishers.

• Chen, H., Fuller, S., Friedman, C., & Hersh, W. (2005). Medical informatics: Knowledge management and data mining in biomedicine. The Netherlands: Springer.

• Goldstein, D., Groen, P., Ponkshe, S., & Wine, M. (2007). Medical informatics 20/20: Quality and electronic health records through collaboration, open solutions, and innovation. New York: Jones & Bartlett.

• Polanski, A., & Kimmel, M. (2007). Bioinformatics. London: Springer.• Shortliffe, E., & Cimino, J. (Eds.). (2006). Biomedical informatics: Computer

applications in health care and biomedicine. London: Springer.• van Bemmel, J., & Musen, M. (Eds.). (1997). Handbook of medical

informatics. The Netherlands: Springer.• Xiong, J. (2006). Essential bioinformatics. Cambridge: Cambridge University

Press.

Biomedical Informatics Literature

• Arp, R. (2007). Philosophical ontology, domain ontology, formal ontology. The Reasoner, 1, 12-13.• Bittner, T., Donnelly, M., & Winter, S. (2006). Ontology and semantic operability. In S. Zlatanova & D.

Prosperi (Eds.), Large-scale 3D data integration: Challenges and opportunities (pp. 139-160). Boca Raton, FL: CRC Press.

• Ceusters, W., Smith, B., & van Mol, M. (2003). Using ontology in query answering systems: Scenarios, requirements and challenges. Proceedings of the 2nd CoLogNET-ElsNET Symposium, Amsterdam, 2, 5-15.

• Grenon, P., & Smith, B. (2004). SNAP and SPAN: Towards dynamic spatial ontology. Spatial Cognition and Computation, 1, 1-10.

• Grenon, P., & Smith, B. (2004a). A formal theory of substances, qualities and universals. In A. Varzi and L. Vieu (Eds.), Proceedings of FOIS 2004. International Conference on Formal Ontology and Information Systems (pp. 49-59). Amsterdam: IOS Press.

• Mars, N. (Ed.). (1995). Towards very large knowledge bases: Knowledge building and knowledge sharing. Amsterdam: IOS Press.

• Menzel, C. (2003). Ontology theory. In J. Euzenat, A. Gomez-Perez, N. Guarino, & H. Stuckenschmidt (Eds.), Ontologies and semantic interoperability (pp. 13-30). Hamburg: IOS Press.

• Smith, B. (2003). Ontology. In L. Floridi (Ed.), Blackwell guide to the philosophy of computing and information (pp. 155-166). Malden, MA: Blackwell.

• Smith, B., & Ceusters, W. (2007). Ontology as the core discipline of biomedical informatics: Legacies of the past and recommendations for the future direction of research. In G. Crnkovic & S. Stuart (Eds.), Computing, philosophy, and cognitive science (pp. 121-145). Cambridge: Cambridge Scholars Press.

• Smith, B., Kumar, A., & Bittner, T. (2004). Basic Formal Ontology for bioinformatics. Available at: http://www.uni-leipzig.de/~akumar/JAIS.pdf.

Domain and Formal Ontology Literature

Thank YouThank You

Robert Arp, Ph.D.Ontology Research Group (ORG)

www.org.buffalo.eduNational Center for Biomedical Ontology

(NCBO)www.bioontology.org

This work was funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant 1 U 54 HG004028. Information on the National Centers for

Biomedical Computing can be found at http://nihroadmap.nih.gov/bioinformatics.