Temporal Data Management: Semantic Web Engineering

1. Temporal Data Management: Semantic Web Engineering Discussion Leader: Cui Tao Assistant Professor in Medical Informatics Mayo Clinic Temporal Reasoning Journal Club December 1, 2011

2. Articles to Discuss • Time-Oriented Question Answering from Clinical Narratives Using Semantic-Web Techniques. Tao C, Solbrig HR, Deepak S, Wei W-Q, Savova G, Chute CG. International Semantic Web Conference, Lecture Note of Computer Science. 2010; 6497:241-56. http://www.springerlink.com/content/67623p256743wv4u/ • Representing Complex Temporal Phenomena for the Semantic Web and Natural Language. Feng Pan, 2007 PhD thesis University of Southern California http://www.isi.edu/~hobbs/time/pub/pan-phdthesis.pdf

3. Why Semantic Web? The Semantic Web provides a suitable environment for temporal data representation and reasoning: • Standard mechanism with explicit and formal semantic definition • OWL DL • SWRL • Reasoning tools, querying and storage mechanisms

4. Ontologies Available Online • Clinical Narrative Temporal Relation Ontology (CNTRO): http://cntro.org/index.html • Time-OWL: http://www.w3.org/TR/owl-time/

5. Goals CNTRO Time-OWL For describing the temporal content of Web pages and the temporal properties of Web services Can also represent structured data • For representing events, time information, and temporal relations in clinical narratives • Can also represent structured data • Presumably can be generalizable

6. Classes CNTRO Time-OWL TemporalEntity Instant Interval ProperInterval DateTimeInterval DurationDescription DateTimeDescription TemporalUnit DayOfWeek • ValidTime • TimeInstant • TimeInterval • TimePeriod • TimePhase • Duration • DurationUnit • Granularity • Event

7. Properties (Time-OWL) Temporal Relations Duration Description DateTime Description

8. Properties (CNTRO)

9. CNTRO Overview

10. Temporal Relations Both adapted Allen's interval algebra Time_OWL CNTRO

11. Duration Time_OWL CNTRO

12. Time Description Time_OWL CNTRO

13. Time-OWLFeatures • Relations for intervals/instants • Time Zones • Day of Week, Day of Year • Specific definition of months, weekdays, etc • Temporal sequence

14. Time-OWL

15. Time-OWL

16. Time-OWL Every other week on Monday, Wednesday and Friday until December 24, 1997, but starting on Tuesday, September 2, 1997. EveryOtherWeek: hasTemporalUnit = unitWeek hasGap = 2 MWFEveryOtherWeek: hasStart = 09/02/1997 hasEnd = 12/24/2007 hasithTemporalUnit =1,3,5 hasTemporalUnit=unitDay hasContextTemporalUnit=unitWeek

17. CNTRO Features • Periodic Time Interval • Relation between Two Events • Time Offset • Relative Time • Uncertainty

18. CNTRORepresentation (Period & Phase) • Example Sentence: take antibiotics every 8 hours for 10 days starting from today (note date:2004-06-01)

19. Operators for Offsets Was e1 before e4? inverse operatorsαand β β(3 days) α(2days) = β (1day)

20. SWRL RuleML • Rule-based Definition for Consistency

21. SWRL RuleML • Rule-based Definition for properties

22. SWRL RuleML • Rule-based Definition for concepts “premature labor after 22 weeks but before 37 completed weeks of gestation without delivery”

23. CNTRO API • findEvent(searchText) • returns a list of events that match the searching criteria. Currently we look for events based on text search. • GetEventFeature(event, featureflag) • returns a specific time feature for a given event. • Sample query: • When was the patient diagnosed with diabetes? • When was the patient started his chemotherapy?

24. CNTRO API • getDurantionBetweenEvents(event1, event2) • returns the time interval between two events. • Sample query: How long after the patient was diagnosed colon cancer did he start the chemotherapy? • getDuration(event) • returns the duration of a given event. • Sample query: How long did the symptoms of rectal bleeding last?

25. CNTRO API • getTemporalRelationType(event1, event2) • returns the temporal relations between two events if it can be retrieved or inferred. • Sample query: Was the PT scan after the colonoscopy? • getTemporalRelationType(event1, time) • returns the temporal relations between an event and a specific time if it can be inferred or retrieved. • Sample query: Is there any behavior change within a week of the test?

26. CNTRO API • sortEventsByTemporalRelationsOrTimeline(events) • returns the order (timeline) of a set of events. • sample query: • What is the tumor status timeline as indicated in the patient’s radiology note? • What is the treatment timeline as recorded in oncology notes? • When was the first colonoscopy done? • When was the most recent glucose test?

27. DiscussionSemantic harmonization Time-related classes harmonization Relation harmonization

28. DiscussionInstances vs. Intervals • Time instant: a time interval with a very short duration • Time interval: a time instant on a coarse level of granularity • “patient’s last cycle of chemotherapy was on Jan. 19” • Process or occurrence? • Interval or instant?

29. DiscussionTemporal Uncertainties • Approximated temporal expression: • In approximately 2 weeks • About 3 hours • In the AM • Late last year • Insufficient level of granularity: • Duration between Jan. and Jun.? • Event A: Jan. and Event B: Jan. 16; what was the temporal relation?

30. DiscussionTemporal Relation on Granularity • “PT WENT INTO CARDIAC ARREST AND THEY WERE UNABLE TO KEEP HEART BEATING FOR MORE THAN A COUPLE HOURS. PT PASSED AWAY THAT NIGHT.” • Cardiac arrest before death (granularity: hour) • Cardiac arrest equal death (granularity: day)

31. DiscussionVague Event Duration • Missing durations is one of the most common sources of incomplete information for temporal reasoning in natural language applications • Empirical approach? • Long, short • Coarse-grained duration information • Set up ranges of durations

32. DiscussionTemporal Uncertainties Coarse temporal notion: • Early next week, middle of last year, short after 11PM, before breakfast • Short after 11:30PM on the 16th, before or on the 17th?

33. DiscussionTemporal Uncertainties Ambiguities: Last cycle of chemotherapy was on Jan. 16. • patient’s last cycle of chemotherapy STARTED on Jan. 19; • patient’s last cycle of chemotherapy ENDED on Jan. 19; • patient’s last cycle of chemotherapy STARTED and ENDED on Jan. 19.

34. Questions