Metamodels

1. Metamodels October, 2012

2. DDI Support for Health Studies

3. DDI-based Health Studies Process Model 4 2 1 3

4. DDI-based Health Studies Process Model 4 2 1 3

5. DDI-based Health Studies Process Model 4 2 1 3

6. DDI-based Health Studies Process Model 4 2 1 3

7. DDI-based Health Studies Process Model 4 2 1 3

8. Contexts and Classifications DDI-based Health Studies Process Model 4 2 1 3

9. DDI-based Health Studies Process Model 4 2 1 3

10. DDI-based Health Studies Process Model 4 2 1 3

11. MDRs Metamodel

12. What is MDRs? • S is for studies • MDRs is at once an application ontology, a metadata database and a website • The metadata database includes a COTS product called Colectica • MDRs uses a second database for biomedical research metadata and other extensions • This second database is not proprietary • It is owned by the National Institutes of Health (NIH) of the United States • The application ontology forms the model • The website accesses the model using the MVC architectural pattern • The website codebase is also owned by the NIH • The codebase is being developed to be reusable across many types of studies

13. What is MDRs? • S is for studies • MDRs is at once an application ontology, a metadata database and a website • The metadata database includes a COTS product called Colectica • MDRs uses a second database for biomedical research metadata and other extensions • This second database is not proprietary • It is owned by the National Institutes of Health (NIH) of the United States • The application ontology forms the model • The website accesses the model using the MVC architectural pattern • The website codebase is also owned by the NIH • The codebase is being developed to be reusable across many types of studies

14. MDRs Architecture (1) • Application ontologies are special purpose ontologies • The special purpose of MDRs is to describe longitudinal health studies and support time series analyses • Because the MDR is an application ontology, however, is not to say that it is “one off” and a dead end • Instead the MDRs application ontology specifically and application ontologies in general have an architecture that makes them reusable From Modularization of Ontologiesby Marek Obitko http://www.obitko.com/tutorials/ontologies-semantic-web/modularization-of-ontologies.html

15. MDRs Architecture (2) • The MDRs application ontology achieves reuse through modularization • Ontologies at lower levels like the MDR Application Ontology import or “borrow from” ontologies at upper levels and then add specific knowledge • MDR borrows concepts from an upper ontology called the Basic Formal Ontology (BFO) • Upper ontologies describe general knowledge like what is time and what is space • Domain ontologies describe a domain like child development, nucleic sequences or the environment From Modularization of Ontologiesby Marek Obitko http://www.obitko.com/tutorials/ontologies-semantic-web/modularization-of-ontologies.html

16. MDRs Architecture (2) • The MDRs application ontology achieves reuse through modularization • Ontologies at lower levels like the MDR Application Ontology import or “borrow from” ontologies at upper levels and then add specific knowledge • MDR borrows concepts from an upper ontology called the Basic Formal Ontology (BFO) • Upper ontologies describe general knowledge like what is time and what is space • Domain ontologies describe a domain like child development, nucleic sequences or the environment From Modularization of Ontologiesby Marek Obitko http://www.obitko.com/tutorials/ontologies-semantic-web/modularization-of-ontologies.html

17. MDRs Architecture (3) • MDRs borrows concepts and concept relationships from at least two domain ontologies – ExO and the NICHD Pediatric Terminology • Finally, task ontologies are instrumental • They often form process models • These process models specify the activities we engage in order to conduct research • There are several well known process models used in the field of bioinformatics including BRIDG (Bioinformatics Research Domain Integrated Group), Life Sciences DAM (Domain Analysis Model), openEHR and HL7 • BRIDG and LS DAM describe the conduct biomedical research From Modularization of Ontologiesby Marek Obitko http://www.obitko.com/tutorials/ontologies-semantic-web/modularization-of-ontologies.html

18. MDRs Architecture (4) • openEHR and HL7 are process models for determining the health of consumers in health care systems • Finally, although it wasn’t designed with biomedical research in mind, DDI Lifecycle is an end-to-end model that “accompanies” and “enables” the conduct of studies • DDI is perhaps the most widely used process model for conducting research in the world • DDI has been adopted as a standard by the World Health Organization, Eurostat and census agencies in North America and across the world • DDI, however, has for the most part been used to describe the conduct of social, behavioral and economic research From Modularization of Ontologiesby Marek Obitko http://www.obitko.com/tutorials/ontologies-semantic-web/modularization-of-ontologies.html

19. MDRs Specifics (1) • The MDR Application Ontology borrows from an upper ontology called the Basic Formal Model. See the BFO Appendix… • It is in the process of integrating a high level environment domain ontology called ExO with the NICHD Pediatric Terminology • “High level domain ontologies” are also referred to as “reference ontologies” • MDR has used ExO to tag exposures, exposure receptors, interventions and exposure outcomes in study questionnaires • It plans to to use the NICHD Pediatric Terminology in connection with neurologic exams and biospecimen data collection From Modularization of Ontologiesby Marek Obitko http://www.obitko.com/tutorials/ontologies-semantic-web/modularization-of-ontologies.html

20. MDRs Specifics (2) • The MDR borrows heavily from the DDI Lifecycle process model • Note that DDI Lifecycle is represented as an XML schema • Both schema-based representations and UML are translatable into frame based models and task ontologies • The MDR uses BFO to divide and structure DDI Lifecycle into two parts: • A set of processes or informatics activities called lifecycle events • And an informatics activities “aggregate” called the DDI Study Model, or, in DDI terminology, “Group” From Modularization of Ontologiesby Marek Obitko http://www.obitko.com/tutorials/ontologies-semantic-web/modularization-of-ontologies.html

21. Appendix Basic Formal Ontology

22. Basic FormalOntology (1) • BFO is widely used to describe phenomena in biomedical research including • Adverse events • Cancer research and management • Biomedical grid terminology • Cell lines and the cell cycle process • The environment • Emotions • Drug interactions • Clinical research • Biomedical investigations • Newborn screening and translational research • Nucleic sequences • Translational medicine • Data mining investigations

23. Basic FormalOntology (2) • BFO is narrowly focused on the task of providing a genuine upper ontology which can be used in support of domain ontologies developed for scientific research • As such BFO does not contain physical, psychological, chemical, biological or other terms • Instead it provides a framework for locating enduring things (continuants) and processes (occurrents) in space time • BFO makes its home at IFOMIS, the Institute for Formal Ontology and Medical Information Science at Saarland University • See http://www.ifomis.org/bfo/home

24. Appendix MDR Application Ontology

25. Descriptive Tags

26. Health Informatics Activity Tags

27. Health Informatics Process Model Tags

28. Health Informatics Activity Coverage