Journal of Medical Systems

, Volume 36, Supplement 1, pp 37–42 | Cite as

Time-Related Patient Data Retrieval for the Case Studies from the Pharmacogenomics Research Network

  • Qian Zhu
  • Cui TaoEmail author
  • Ying Ding
  • Christopher G. Chute
Original Paper


There are lots of question-based data elements from the pharmacogenomics research network (PGRN) studies. Many data elements contain temporal information. To semantically represent these elements so that they can be machine processiable is a challenging problem for the following reasons: (1) the designers of these studies usually do not have the knowledge of any computer modeling and query languages, so that the original data elements usually are represented in spreadsheets in human languages; and (2) the time aspects in these data elements can be too complex to be represented faithfully in a machine-understandable way. In this paper, we introduce our efforts on representing these data elements using semantic web technologies. We have developed an ontology, CNTRO, for representing clinical events and their temporal relations in the web ontology language (OWL). Here we use CNTRO to represent the time aspects in the data elements. We have evaluated 720 time-related data elements from PGRN studies. We adapted and extended the knowledge representation requirements for EliXR-TIME to categorize our data elements. A CNTRO-based SPARQL query builder has been developed to customize users’ own SPARQL queries for each knowledge representation requirement. The SPARQL query builder has been evaluated with a simulated EHR triple store to ensure its functionalities.


Temporal ontology Semantic web Pharmacogenomics studies SPARQL query builder 



This work was partially supported by the NIH/NIGMS (U19 GM61388; the Pharmacogenomic Research Network, PGRN) and the Strategic Health IT Advanced Research Projects (SHARP) Program (90TR002) administered by the Office of the National Coordinator for Health Information Technology. The contents of the manuscript are solely the responsibility of the authors.

Conflict of Interest

The authors declare that they have no conflict of interest.


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Copyright information

© Springer Science+Business Media New York 2012

Authors and Affiliations

  • Qian Zhu
    • 1
  • Cui Tao
    • 1
    Email author
  • Ying Ding
    • 2
  • Christopher G. Chute
    • 1
  1. 1.Mayo ClinicRochesterUSA
  2. 2.Indiana UniversityBloomingtonUSA

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