Building a semantic web-based metadata repository for facilitating detailed clinical modeling in cancer genome studies

Guoqian Jiang, Deepak K. Sharma, Harold Solbrig, Cui Tao, Chunhua Weng, Christopher Chute

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

Detailed Clinical Models (DCMs) have been regarded as the basis for retaining computable meaning when data are exchanged between heterogeneous computer systems. To better support clinical cancer data capturing and reporting, there is an emerging need to develop informatics solutions for standardsbased clinical models in cancer study domains. The objective of the study is to develop and evaluate a use case-driven approach that enables a Semantic Webbased cancer study metadata repository based on both ISO11179 metadata standard and Clinical Information Modeling Initiative (CIMI) Reference Model (RM). We used the common data elements (CDEs) defined in The Cancer Genome Atlas (TCGA) data dictionary, and extracted the metadata of the CDEs using the NCI Cancer Data Standards Repository (caDSR) CDE dataset rendered in the Resource Description Framework (RDF). The ITEM/ITEM-GROUP pattern defined in the latest CIMI RM is used to represent reusable model elements (mini-Archetypes). We performed a case study of the domain "clinical pharmaceutical" in the TCGA data dictionary to demonstrate the clinical utility of our approach. We produced a metadata repository with 38 clinical cancer genome study domains, comprising a rich collection of mini-Archetype pattern instances. In summary, our informatics approach leveraging Semantic Web technologies provides an effective way to build a CIMIcompliant metadata repository that would facilitate the detailed clinical modeling to support use cases beyond TCGA in clinical cancer study domains.

Original languageEnglish (US)
Title of host publicationSWAT4LS 2014 - Proceedings of the 7th International Workshop on Semantic Web Applications and Tools for Life Sciences
PublisherCEUR-WS
Volume1320
Publication statusPublished - 2014
Externally publishedYes
Event7th International Workshop on Semantic Web Applications and Tools for Life Sciences, SWAT4LS 2014 - Berlin, Germany
Duration: Dec 9 2014Dec 11 2014

Other

Other7th International Workshop on Semantic Web Applications and Tools for Life Sciences, SWAT4LS 2014
CountryGermany
CityBerlin
Period12/9/1412/11/14

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Keywords

  • Cancer studies
  • Clinical information modeling initiative (CIMI)
  • Common data elements (CDEs)
  • Detailed clinical models (DCMs)
  • Semantic web technologies
  • The cancer genome atlas (TCGA)

ASJC Scopus subject areas

  • Computer Science(all)

Cite this

Jiang, G., Sharma, D. K., Solbrig, H., Tao, C., Weng, C., & Chute, C. (2014). Building a semantic web-based metadata repository for facilitating detailed clinical modeling in cancer genome studies. In SWAT4LS 2014 - Proceedings of the 7th International Workshop on Semantic Web Applications and Tools for Life Sciences (Vol. 1320). CEUR-WS.