1. Review of OWL for Biomedicine - II Alan Rector & CO-ODE/NIBHI University of Manchester Rector@cs.man.ac.uk OpenGALEN BioHealth Informatics Group © University of Manchester

2. 2 Pneumonia, Pneumonitis, and Infection ►“Pneumonia” is really an infection not just an inflammation. ►At least according to most dictionaries - again separate words and meaning. ►“Pneumonitis” is more properly an inflammation of the lung ►Pneumonia is an inflammation of the lung caused by an infection ►And if we want to be more pedantic we might want to make inflammation something like ‘generalised inflammation’ to distinguish it from abscess, ulcer, and other inflammatory processes ►SNOMED-CT doesn’t bother ►What granularity depends on application

3. © University of Manchester 3 So define “Pneumonitis” extend the definition of Pneumonia Add infectious pneumonitis Pneumonitis Infectious pneumonitis Pneumonia redefined

4. © University of Manchester 4 Classify ►“Pneumonia” ≡ “Infectious_pneumonitis” ►As it should be. The two definitions are equivalent ►Pure_bacterial_pneumonia is inconsistent ►Why?

5. © University of Manchester 5 Look for yourself ►Hint: ►Bugs after re-arranging the ontology are most often due to violation of disjoint axioms ►Use OwlViz to check disjoints

6. © University of Manchester 6 Using OwlViz to track disjoints Infection and Bacterium are disjoint

7. © University of Manchester 7 Or use the debugger: ‘Heuristic” but usually finds the problem ►Text from Debugger ►The universal restriction means that all relationships along hasCause must be to individuals that are members of Bacterium However, the existential restriction means that there must be at least one relationship to an individual from Infection, which is disjoint from Bacterium. ►Display from debugger

8. © University of Manchester 8 What to do ►Bacterium and Infection are clearly disjoint ►Do not want to distort the ontology ►Therefore must change the restrictions ►What causes what ►Inflammation is has_causal_process SOME Infection has_causitive_agent SOME Bacterium ►has_cause is clearly too broad a property ►Things can have a causal process by agents or processes ►Processes can have a causitive agent ►(Might want “creative blurring” and to allow Things to have causitive agents - but leave that for later.)

9. © University of Manchester 9 Modify Properties and definitions to eg ►Mixed Pneumonia ►Pure_bacterial_pneumonia ►Properties

10. © University of Manchester 10 Classify and re-run unit tests ►NB: failures spurious - only checks for direct superclasses. To be fixed RSN.

11. © University of Manchester 11 Anonymous and named classes ►OWL allows a choice of either anonymous embedded classes (bracketing) ►Either: Pneumococcal_pneumonia is a Pneumonia THAT has causitive process some Infection THAT has causitive agent Pneumococcus ►Or: Pneumococcal_pneumonia is a Pneumonia THAT has causitive process some Pneumococcal_infection ►And: Pneumococcal_infection is an Infection THAT has causitive agent Pneumococcus

12. © University of Manchester 12 The meaning is the same, … but beware ►It is easy to create subtly different concepts when using named notions ►The naming can hide the bracketing ►May need transformations, intermediate representations, or “close to user forms” ►E.g. “Left Chest X-Ray” is an “X-Ray of the Left Chest” rather than a “Left sided X-Ray of the Chest” ►Check it with the classifier

13. © University of Manchester 13 Value partitions and “Severe Pneumonia” ►Create the Value Partion for Severity ►Create a new Value_partition and partition it ►Severity_value_partition Severe_severity_value Moderately_severe_value Mild_severity_value ►Internally it is usually better to use fully disambiguated names ►What shows in the application can be whatever is convenient. ►Make the partitioning disjoint and covering See SWBP http://www.w3.org/TR/swbp-specified-values/http://www.w3.org/TR/swbp-specified-values/

14. © University of Manchester 14 Value partitions II ►Create the property for has_severity ►Make it functional (single valued) ►Give it a range of “Severity_value_partition” ►Give it a domain of “Disorder” (There is a wizard to do all this)

15. © University of Manchester 15 Define Severe Pneumonia ►Remember: The definition is not complete without a text comment ►We haven’t really ‘defined’ severe pneumonia at all, merely created a place in the classification for it

16. © University of Manchester 16 What it means ►A severe pneumonia is one whose severity is from the severe part of the value partition Pneumonia Severe_ Pneumonia Severity_VP Severe_ value(s) Moderate value(s) Mild_ value(s)

17. © University of Manchester 17 UML Style pattern(from SWBP) Severe_Pnuemonia Mild_severity Moderate_severity Severe_severity Severity_VP Pneumonia & has_severity

18. © University of Manchester 18 Simple localisation to parts: “Lobar Pneumonia” ►Pneumonia of a lobe of the lung ►Classify and check ►Seems OK ►… but consider “Inflammation caused by infection of locus some lobe of lung” ►Does not even come out as a kind of Pneumonia

19. © University of Manchester 19 What is wrong ►Lobes are not lungs ►Lobes of lungs are parts of lungs not kinds of lungs ►“Pneumonia” does not have to involve the entire lung ►has_locus “Lung or a part of a lung” ►Now classifies correctly and passes unit test.

20. © University of Manchester 20 A chest X-Ray showing Pneumonia: Model of meaning ►How to represent a chest X-Ray showing pneumonia ►The things in the patient - Lung, etc. ►The technique - PA | Lateral | AP … ►The image/film ►The artifacts on the image - Opacities, Densities, Shadows ►Ambiguous - Costo-Phrenic Angle - ►The anatomists claim it doesn’t exist except as a shadow ►The Interpretation - what the doctor believes believes the X- Ray shows about the patient - Pneumonia, Improvement, …

21. © University of Manchester 21 Choices ►What to make the central item to classify ►Interpretation of Artifacts on Image taken by Technique of site (Anatomical_entity? Thing? …) ►The image? ►The interpretation? ►Other? ►For what purpose? For whom? ►OWL will guarantee that all views are consistent ►But has no way to say that two things are the same

22. © University of Manchester 22 Fit to medical record Still at level of meaning ►Patient is reported to have Condition as determined by Procedure ►Patient is reported to have Disorder with locus site as determined by Image taken by Technique of site for a Reason showing signs ► There is no one way! ►… but for demonstration purposes we have to choose ►As for any implementation ►But one view can be transformed to another ►Co-ordinate systems are important, but you don’t go to war over them

23. © University of Manchester 23 Key issue: Maintain orthogonal axes “Normalisation” ►First work out what you can say ►Then the constraints on what you can’t ►So start with the existential graph ►What do we want to be sure to retrieve together ►X-Rays interpreted as showing pneumonia? ►Pneumonias however diagnosed? As diagnosed by X-Ray? ►X-rays of Chest? ►P-A X-Rays of chest? ►X-rays showing opacities ►What is essential? What is ‘ontological’ - about meaning ►What are the consequences of decisions ►Science not religion

24. © University of Manchester 24 Experiment! Two possible entities ►“Pneumonia shown on Radiograph of Chest showing consolidation” ►“Radiograph interpreted as Pneumonia showing consolidation” ►(You substitute the sign for “consolidation”) ►Whichever we will need ►Radiographic_entities - studies, etc. ►Radiographic_signs - opacities, etc. ►Radiographic_techniques - PA, Lateral etc. ►We’ll keep for now ►Disorders, Anatomy, Etc.

25. © University of Manchester 25 One variant: ►Note: We could have named the subenjtities, e.g. “PA-Lateral Radiographic Technique” “Opacity indicating Consolidation” ►Note that for this experiment we have created a new file and imported the original bio file which has namespace “bio:”

26. © University of Manchester 26 Same example with named classes ►Classifies as equivalent ►Ontology: Radiology-example-01

27. © University of Manchester 27 Alternative experiment “Qua induction” “Dual” ►OWL will impose the same constraints on both

28. © University of Manchester 28 A possible bug ►Suppose the domain of has_exam_position were accidentally set to Radiographic_study instead of Radiographic_technique ►Lots of Red ►Errors propagate ►A single source ►But they propagate consistently ►Both “duals” are inconsistent - Radiograph & Pneumonia source

29. © University of Manchester 29 What to do when “Its all turned red” ►Unsatisfiability propagates – so trace it to its source ►Any class with an unsatisfiable filler in a someValuesFor (existential) restriction is unsatisfiable ►Any subclass of an unsatisfiable class is unsatisfiable ►Only a few possible sources ►Violation of disjoint axioms ►Unsatisfiable expressions in some restrictions ►Confusion of “and” and “or” ►Violation of a universal (allValuesFrom) constraint (including range and domain constraints) ►Check domain and range constraints first ►Try the debugger ►It’s not perfect but it finds most thing Don’t Panic!

30. © University of Manchester 30 Which representation to choose: ►What’s the task ►(My understanding) To construct forms for reports ►Therefore focus on th0e in the first instance in the radiograph ►An an ontology for reports/forms

31. © University of Manchester 31 Create a new ontology for Forms ►I have done it here in a separate ontology and imported for modularity ►Top bio ►Radiology ►Forms

32. © University of Manchester 32 Form for radiograph ►Any form for a radiographic study requires exactly one subform for technique ►Any form for a CXR must have an appropriate technique and subforms for Heart and Lung Fields

33. © University of Manchester 33 Or could be abbreviated by providing suitable definitions

34. © University of Manchester 34 And from a different view expanded along existential restrictions for different views or trees Ontology Class diagram view Contents Use/Activity View

35. © University of Manchester 35 Why go to so much trouble? ►Modularity ►Scaling ►Consistency ►Maintainability & smooth evolution ►Transparency ►But it is not the standard use of OWL for terminologies ►And it does require some additional mechanisms