Ontology and Rad Lex Robert Arp Ph D

Ontology and Rad. Lex Robert Arp, Ph. D. Ontology Research Group (ORG) www. org. buffalo. edu National 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 HG 004028. 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 Rad. Lex

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 Rad. Lex

Rad. Lex: A Lexicon for Uniform Indexing and Retrieval of Radiology Information Resources

Rad. Lex: 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

Thing Immaterial Substance Material Substance Animate (Living) Entity Living Entity with Sensation (Animal) Rational Animal (Human) Non-Animate Entity Living Entity without Sensation (Vegetation) Non-Rational Animal

Thing Immaterial Substance Material Substance Animate (Living) Entity Living Entity with Sensation (Animal) Rational Animal (Human) Non-Animate Entity Living Entity without Sensation (Vegetation) Non-Rational Animal PORPHYRIAN TREE Compare: Linnean Taxonomy and Periodic Table

Sub-types (children) should inherit all the features of the relevant type (parent) Thing Animate (Living) Entity Living Entity with Sensation (Animal) Rational Animal (Human) Immaterial Substance Material Substance Non-Animate Entity Living Entity without Sensation (Vegetation) Non-Rational Animal PORPHYRIAN TREE Compare: Linnean Taxonomy and Periodic Table

Sub-types(children) shouldinheritallallthe features of the relevant features of the type (parent) along relevant type (parent) with some differentia (distinguishing feature) Thing Material Substance Immaterial Substance A is_a. Non-Animate BEntity that/which Cs PORPHYRIAN Animate (Living) Entity A is_a B that/which. TREE has Cs - rational animal (A) is_a living entity with. Compare: sensation (B) that Linneanfor Taxonomy has the capacity conscious and Periodic Table Non-Rationalthinking (C) Living Entity without Sensation (Vegetation) Living Entity with Sensation (Animal) Rational Animal (Human) Animal

A is_a B that/which Cs A 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 (Env. O) 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 Ontology hybrid of: - Glossary - Catalogue - Taxonomy - Various Relations - Inventory - Axiomatic Rules of - Axiomatic Theory Inference - Simple Taxonomy

Domain ontology contrasted with: - Database - Rule-Based Language - Thesaurus Rad. Lex, as of now, - Glossary is a thesaurus of - Catalogue terms, although - Inventory confuses terms and entities those terms - Axiomatic Theory refer to… - Simple Taxonomy

Basic Mouse Trap Classification Simple Taxonomy: is_a, sub-type relation

Beginnings of Mouse Trap Domain Ontology

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…

SILO EFFECT

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

From this… To this…

Basic Formal Ontology (BFO)

REALISM-BASED ONTOLOGY Universals (1) real objects, substances, endurants, or continuants - SNAP shots of reality (2) real processes, activities, perdurants, or occurrents - SPAN of time Relations is_a, part_of, has_participant. . .

ti m e continuants vs. occurrents continuant (substance, object) occurrent (process) In classifying parts of reality, we keep track of these two different kinds of entities in two different ways

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 objects, qualities, functions - 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 processes, activities

continuant Relation: is_a Sub-types (children) should inherit all the features of the relevant type (parent)

continuant HUMAN HEART 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 prop in a display

occurrent Relation: is_a

occurrent ECG/EKG TEST ECG/EKG ECG (EKG) test start/end of ECG all ECGs in clinic 2 nd lead attached activities in clinic s/t ECG began moment ECG began s/t region of ECG time occupied

(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 Rad. Lex (although, Rad. Lex 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 Rad. Lex

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 Rad. Lex 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 Rad. Lex 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 Rad. Lex term? Is an infusion a Rad. Lex 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 Rad. Lex 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 Rad. Lex composed of terms)

Three Levels to Keep Straight Cognitive representations Representational artifacts Reality

Radiology and Ontology Literature - 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/ 978708 n 776738132/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.

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.

Biomedical Informatics Literature • 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.

Domain and Formal Ontology 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 3 D 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 2 nd Co. Log. NET-Els. NET 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. (2004 a). 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.

Thank You Robert Arp, Ph. D. Ontology Research Group (ORG) www. org. buffalo. edu National 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 HG 004028. Information on the National Centers for Biomedical Computing can be found at http: //nihroadmap. nih. gov/bioinformatics.