1 / 17

A Semantic-Web Representation of Clinical Element Models

A Semantic-Web Representation of Clinical Element Models. Cui Tao, PhD Mayo Clinic. Acknowledgement. Christopher G. Chute, MD, DrPH Robert R. Freimuth , PhD Stanley M. Huff, MD Guoqian Jiang, PhD Thomas A. Oniki , PhD Jyotishman Pathak , PhD Craig Parker, MD Deepak Sharma

lotta
Télécharger la présentation

A Semantic-Web Representation of Clinical Element Models

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  1. A Semantic-Web Representation of Clinical Element Models Cui Tao, PhD Mayo Clinic

  2. Acknowledgement • Christopher G. Chute, MD, DrPH • Robert R. Freimuth, PhD • Stanley M. Huff, MD • Guoqian Jiang, PhD • Thomas A. Oniki, PhD • JyotishmanPathak, PhD • Craig Parker, MD • Deepak Sharma • FeichenShen • Sridhar D. Yadav • QianZhu, PhD

  3. EHR SHARPn drools Normalized EHR XML Database Schema XML Schema CEM Database OWL Triple Store SWRL drools

  4. Introduction Clinical Element Model (CEM): • Logical models ensure semantic interoperability for: • Data representation • Data interpretation • Data exchange within and across heterogeneous sources and applications • Represented in CEML/CDL (Constraint Definition Language) • Define syntax and grammar • Not semantics

  5. Introduction Semantic Web • Explicit and formal semantic knowledge representation • Web Ontology Language (OWL) /Resource Description Framework (RDF): • Define relationships • Define classes • Define constraints • Consistency checking • Link to other domain terminologies • Harmonize with other clinical data modeling languages • Semantic reasoning

  6. Layer1:meta-ontology Meta-CEM.OWL Layer2: detailed clinical element models Detailed Clinical Element Model Ontology Layer3:patient instances RDF Triple Store Joe Doe’s record Jean Doe’s record Joe Doe’s record

  7. Semantic Reasoning • Consistency checking • Cardinality constraints • Data types • Property allowed domains and ranges • Permissible values in value sets • Classification and reasoning

  8. Consistency Checking

  9. Consistency Checking

  10. Consistency Checking

  11. Automatic Classification Semantic Definition of Normal DBP Data Two DBP Measurements

  12. Automatic Classification Semantic Definition of Normal BP Infer that both exam1 and exam2 are within the normal range

  13. Semantic Reasoning Example Has two outpatient (if possible) measurements of SBP >140 or DBP > 90 at least one month after taking anti-hypertensive drugs. Ontology: “Labetalol 100mg” (SCT318445000) is an anti-hypertensive drug (SCT1182007). CNTRO temporal relation reasoner: 5 weeks > one month Duration (May 1 and March 1) > one month

  14. Implementation Status • Meta Ontology • Basic category classes • Properties • Cardinality constraints • Two OWL experts and two CEM experts have evaluated the meta-ontology to ensure it can faithfully cover the original contents • Automatic Convertor: detailed CEM ontologies

  15. CEM-OWL convertor Meta-Ontology import Shared CEM Ontology import CEM Core Model Ontologies import CEM Secondary Use Ontologies

  16. Download the ontologies • Shared Models:http://informatics.mayo.edu/sharp/CEM2OWL/CEM-Shared.owl • CORE Models:http://informatics.mayo.edu/sharp/CEM2OWL/COREModels/COREStandardLabObs.owlhttp://informatics.mayo.edu/sharp/CEM2OWL/COREModels/COREStandardLabObsCoded.owlhttp://informatics.mayo.edu/sharp/CEM2OWL/COREModels/COREStandardLabObsIntervalQuantitative.owlhttp://informatics.mayo.edu/sharp/CEM2OWL/COREModels/COREStandardLabObsNarrative.owlhttp://informatics.mayo.edu/sharp/CEM2OWL/COREModels/COREStandardLabObsOrdinal.owlhttp://informatics.mayo.edu/sharp/CEM2OWL/COREModels/COREStandardLabObsQuantitative.owlhttp://informatics.mayo.edu/sharp/CEM2OWL/COREModels/COREPatient.owlhttp://informatics.mayo.edu/sharp/CEM2OWL/COREModels/CORENotedDrug.owlhttp://informatics.mayo.edu/sharp/CEM2OWL/COREModels/COREDiseaseDisorder.owl • Secondary Use:http://informatics.mayo.edu/sharp/CEM2OWL/SecondaryUse/SecondaryUseDiseaseDisorder.owlhttp://informatics.mayo.edu/sharp/CEM2OWL/SecondaryUse/SecondaryUseNotedDrug.owlhttp://informatics.mayo.edu/sharp/CEM2OWL/SecondaryUse/SecondaryUsePatient.owlhttp://informatics.mayo.edu/sharp/CEM2OWL/SecondaryUse/SecondaryUseStandardLabObsCoded.owlhttp://informatics.mayo.edu/sharp/CEM2OWL/SecondaryUse/SecondaryUseStandardLabObsIntervalQuantitative.owlhttp://informatics.mayo.edu/sharp/CEM2OWL/SecondaryUse/SecondaryUseStandardLabObsNarrative.owlhttp://informatics.mayo.edu/sharp/CEM2OWL/SecondaryUse/SecondaryUseStandardLabObsOrdinal.owlhttp://informatics.mayo.edu/sharp/CEM2OWL/SecondaryUse/SecondaryUseStandardLabObsQuantitative.owlhttp://informatics.mayo.edu/sharp/CEM2OWL/SecondaryUse/SecondaryUseStandardLabObsTiter.owl

  17. Conclusion and Future Directions • Meta-Ontology: semantically defined the basic classes, properties, their relationships, and constraints • Convertor: CDLOWL • Represent SHARPn normalized data using RDF • Investigate SWRL/Drools combination for phenotyping

More Related