ontology and radlex robert arp, ph.d
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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.