Metamodels

Metamodels

October, 2012

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DDI SUPPORT FOR HEALTH STUDIES

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DDI-based Health Studies Process Model

• Enumerate study concepts

• Select corresponding common data elements (CDEs) for use in instruments

• Define sampling strategy

• Define study protocol

• Specify administrative data elementsStudy

Definition

• Identify extant data sources

• Develop instruments

• Specify assays and analytes

• Execute sampling strategy

• Schedule data collections

• Execute data collections

• Record administrative data

Data Collection

• Identify data elements that are still not standardized

• Construct and propose additional candidate CDEs

• Migrate collected data into variables corresponding to CDEs

• Link extant and instrument data Data

Aggregation

• Classify CDEs using medical subject headers (MeSH)

• Tag CDEs with one or more domain ontologies

• Discover study using CDE and domain ontology browsers

• Order variables from order fulfillment service

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http://kr-med.org/icbofois2012/vdosme/docs/papers/icbo-2012_submission_106_Burns.pdf

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http://noteandpoint.com/2010/04/nosql-for-fun-profit/

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MDRS METAMODEL

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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

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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

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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

Upper Ontology

Task Ontology

Application Ontology

Domain Ontology

From Modularization of Ontologiesby Marek Obitko

http://www.obitko.com/tutorials/ontologies-semantic-web/modularization-of-ontologies.html

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• 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

Upper Ontology

Task Ontology


Domain Ontology



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• 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

Upper Ontology

Task Ontology


Domain Ontology



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– 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

Upper Ontology

Task Ontology


Domain Ontology



http://bioportal.bioontology.org/ontologies/45220?p=terms

http://bioportal.bioontology.org/ontologies/1640

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– 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

Upper Ontology

Task Ontology


Domain Ontology



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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

BFO

DDI Study Model

MDRs

ExO Pediatric

Terminology



http://bioportal.bioontology.org/ontologies/45220?p=terms

http://bioportal.bioontology.org/ontologies/1640

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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”

BFO

DDI Study Model

MDRs

ExO Pediatric

Terminology



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BASIC FORMAL ONTOLOGYAppendix

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Basic Formal Ontology (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

http://www.ifomis.org/bfo/users

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Basic Formal Ontology (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

http://www.ifomis.org/bfo/home

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MDR APPLICATION ONTOLOGYAppendix

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Descriptive Tags

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Health Informatics Activity Tags

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Health Informatics Process Model Tags

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Health Informatics Activity Coverage

Documents

Metamodels