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Challenges In Transforming Observational Data For Analysis

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  1. Challenges In Transforming Observational DataFor Analysis OR How To Call Into QuestionYour Observational Data Without Even Trying Don Griffin Health Informatics Technology Director Computer Sciences Corporation May 20, 2009

  2. Objectives Lofty Objective: Present a complete health Informatics solution: • that is flexible enough to accommodate all of the types of source data that end users will require—even if they do not know what those data will be—and • that is rich enough in functionality to support all of the data transformations and manipulations that end users will require to convert those source data into research-oriented knowledge on which they may confidently rely. More Practical Objective: Leave those in the audience with an appreciation for the things that must be done ahead-of-time to make multifarious, disparate, observational source data sets useful for analysis.

  3. Definitions Observational Data • “... the outcomes of acts of measurement using particular protocols within the context of any objective scientific measurement activity.” • “… the basic or atomic notion of an observation represents: • the outcome of some measurement taken of a defined attribute or characteristic of some ‘entity’ (e.g., an organism ‘in the field,’ a specimen, a sample, an experimental treatment, etc.), • within some context (possibly given by other observations).” • “Every observation entails the measurement of one or more properties of some real-world entity or phenomenon.” Biodiversity Information Standards – TDWG For Our Purposes: • we are most interested in observational data on drug exposures and medical conditions (but other data may interest us, too), and • chief sources will be Medical Claims and Electronic Health Records (EHRs).

  4. Definitions Data Transformation • “... the operation of changing (as by rotation or mapping) one configuration or expression into another in accordance with a mathematical rule; especially: a change of variables or coordinates in which a function of new variables or coordinates is substituted for each original variable or coordinate…” • “… an operation that converts (as by insertion, deletion, or permutation) one grammatical string (as a sentence) into another…” Merriam-Webster’s Dictionary • One of the three pillars of data governance (along with compliance and integration). “… transformation is a goal unto itself, as well as an enabler for the goals of compliance and integration.” The Data Warehousing Institute • For Our Purposes: • we are most interested in reformatting data into a Common Data Model that allows portability of analysis methods across disparate source data sets, and • in standardizing data representations to make analysis results from disparate source data sets readily comparable.

  5. Transforming Observational Data Again, for our purposes, the process is rather simple. However, to do it correctly presents some challenges.

  6. Transforming Observational Data Again, for our purposes, the process is rather simple. However, to do it correctly presents some challenges.

  7. The IT View of the End User’s Goal Skillful use of Common Data Model content to communicate “complex ideas… with clarity, precision, and efficiency” (and, ideally, unimpeachability ) • Show the data • Induce the viewer to think about the substance rather than about methodology, graphic design, the technology of graphic production, or something else • Avoid distorting what the data have to say • Present many numbers in a small space • Make large data sets coherent • Encourage the eye to compare different pieces of data • Reveal the data at several levels of detail, from a broad overview to the fine structure • Serve a reasonably clear purpose: description, exploration, tabulation, or decoration • Be closely integrated with the statistical and verbal descriptions of a data set Edward Tufte, The Visual Display of Quantitative Information

  8. The IT View of IT’s Goals Provide services necessary to populate the Common Data Model • Data Architecture • Data Collection • Data Extraction, Transformation, and Loading (ETL) • Data Management Help (or do not hinder) end users in pursuit of their own goals • Preserve the data (i.e., their native values, formats, etc.) • Avoid distorting the data • Maintain data detail Foster the widespread understanding of the data • What the data are and are not • What the data can and cannot do

  9. IT Issues/Challenges Source Target (CDM) DataManagement Technical DataCollection ETL Design DataArchitecture DataUnderstanding Philosophical

  10. IT Issues/Challenges Data Collection • Batch vs. Stream • Reception and Profiling • Verification to Specification • Culling and Cleansing • Staging

  11. Profiling

  12. Verification to Specification

  13. Profiling

  14. Profiling

  15. Verification to Specification

  16. IT Issues/Challenges Data Management • Inventory and Tracking • Privacy, Security, and Compliance • Master/Reference Data Management • Logging and Auditing

  17. Privacy Protected Health Information • Any information (not just textual data) in the medical record or designated data set that can be used to identify an individual, and • That was created, used, or disclosed in the course of providing a health care service (e.g., diagnosis, treatment, etc.) HIPAA regulations allow researchers to access and use PHI when necessary to conduct research. However, HIPAA only affects research that uses, creates, or discloses PHI that will be entered in to the medical record or that will be used for the provision of heath care services (e.g., treatment). • Research studies involving review of existing medical records for research information, such as retrospective chart review, are subject to HIPAA regulations. • Research studies that enter new PHI into the medical record (e.g., because the research includes rendering a health care service, such as diagnosing a health condition or prescribing a new drug or device for treating a health condition) are also subject to HIPAA regulations. • If in doubt, stay away from the 18 “identifiers.”

  18. Privacy 18 Identifiers 1. Names; 2. All geographical subdivisions smaller than a State, including street address, city, county, precinct, zip code, and their equivalent geocodes, except for the initial three digits of a zip code, if according to the current publicly available data from the Bureau of the Census: (1) The geographic unit formed by combining all zip codes with the same three initial digits contains more than 20,000 people; and (2) The initial three digits of a zip code for all such geographic units containing 20,000 or fewer people is changed to 000. 3. All elements of dates (except year) for dates directly related to an individual, including birth date, admission date, discharge date, date of death; and all ages over 89 and all elements of dates (including year) indicative of such age, except that such ages and elements may be aggregated into a single category of age 90 or older; 4. Phone numbers; 5. Fax numbers; 6. Electronic mail addresses; 7. Social Security numbers;

  19. Privacy 18 Identifiers 8. Medical record numbers; 9. Health plan beneficiary numbers; 10. Account numbers; 11. Certificate/license numbers; 12. Vehicle identifiers and serial numbers, including license plate numbers; 13. Device identifiers and serial numbers; 14. Web Universal Resource Locators (URLs); 15. Internet Protocol (IP) address numbers; 16. Biometric identifiers, including finger and voice prints; 17. Full face photographic images and any comparable images; and 18. Any other unique identifying number, characteristic, or code (note this does not mean the unique code assigned by the investigator to code the data)

  20. Privacy De-identification is a possible solution. However, additional standards and criteria apply. • Any code used to replace the identifiers in datasets cannot be derived from any information related to the individual and the master codes, nor can the method to derive the codes be disclosed. For example, a subject's initials cannot be used to code his data because the initials are derived from his name. • The researcher must not have actual knowledge that the subject could be re-identified from the remaining identifiers in the PHI used in the research study. That is, the information would still be considered identifiable is there was a way to identify the individual even though all of the 18 identifiers were removed.

  21. Privacy The following is NOT considered PHI, and therefore is not subject to HIPAA regulations. • Health information absent the 18 identifiers. • Data that would ordinarily be considered PHI, but which are not associated with or derived from a healthcare service event (treatment, payment, operations, medical records), not entered into the medical record, and not disclosed to the subject. Research health information that is kept only in the researcher’s records is not subject to HIPAA, but is regulated by other human subjects protection regulations. Examples of research health information not subject to HIPAA include such studies as the use of aggregate data, diagnostic tests that do not go into the medical record because they are part of a basic research study and the results will not be disclosed to the subject, and testing done without the PHI identifiers. • Some genetic basic research can fall into this category such as the search for potential genetic markers, promoter control elements, and other exploratory genetic research. • In contrast, genetic testing for a known disease that is considered to be part of diagnosis, treatment and health care would be considered to use PHI and therefore subject to HIPAA regulations. University of California, Berkeley Committee for Protection of Human Subjects

  22. IT Issues/Challenges Data Extraction • Form (e.g., ASCII vs. EBCDIC) • Format (e.g., delimited, fixed-length, ragged right, etc.) Data Transformation • Reformatting (usually from flat to relational) • Probabilistic Matching • Augmentation (excluding Standardization) • Master <fill in the blank> Indexing • Standardization Data Loading

  23. Person Timeline Drug A A1 A2 A3 A4 Persistence window DrugEra1 B1 B2 Drug B Persistence window DrugEra2 DrugEra3 Person Timeline Condition A A1 A2 A3 A4 ConditionEra1 B1 B2 Condition B Persistence window ConditionEra2 ConditionEra3 Augmentation

  24. Standardization

  25. IT Issues/Challenges Data Architecture • Common Data Model Design Paradigms • “All models are wrong, but some are useful” George Box, Statistician • Flexibility vs. Intuitiveness “Compromise”

  26. OMOP Common Data Model (conceptual)

  27. OMOP Common Data Model (logical)

  28. Solution Framework CORE BUSINESS INTELLIGENCE SERVICES Statistical Analysis and Validation Reports/ Dashboards Process Models OLAP, ROLAP MOLAP, HOLAP Business Rules/Predictive Models Queries Optimization FOUNDATIONAL DATA SERVICES Data Architecture SUPPORTING SERVICES Business Integration Services Presentation and Portal Services Systems Management Services Database Management System Data Models Metadata Data Collection Data Integration Data Management Verification to Specification Reception and Profiling Probabilistic Matching Inventory and Tracking Privacy, Security, and Compliance Augmentation Controlled Medical Vocabularies Staging for Integration Master Person Indexing Culling and Cleansing Logging and Auditing Master/Reference Data Maintenance

  29. Solution Context OVERALL SOLUTION STEWARDSHIP Strategy Process Intelligence Governance LIFE SCIENCES SOLUTIONS Scientific Applications Operational Reporting Marketing Study Recruitment Drug Safety Monitoring Site Management Clinical Data Management Market Intelligence Exploratory Data Analysis Study Management Protocol Feasibility Health Outcomes & Economics Licensing Intelligence Drug Safety Management Executive Dashboards Closed Loop Marketing CORE BUSINESS INTELLIGENCE SERVICES Statistical Analysis and Validation Reports/ Dashboards Process Models OLAP, ROLAP MOLAP, HOLAP Business Rules/Predictive Models Queries Optimization FOUNDATIONAL DATA SERVICES Data Architecture SUPPORTING SERVICES Business Integration Services Presentation and Portal Services Systems Management Services Database Management System Data Models Metadata Data Collection Data Integration Data Management Verification to Specification Reception and Profiling Probabilistic Matching Inventory and Tracking Privacy, Security, and Compliance Augmentation Controlled Medical Vocabularies Staging for Integration Master Person Indexing Culling and Cleansing Logging and Auditing Master/Reference Data Maintenance

  30. Thank You Don Griffin (dgriffin2@csc.com) Health Informatics Technology Director Computer Sciences Corporation May 20, 2009