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Development of the Lymphoma Enterprise Architecture Database: A caBIG Silver Level Compliant System

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Development of the Lymphoma Enterprise Architecture Database: A caBIG Silver Level Compliant System

Taoying Huang et al. Cancer Inform.

Abstract

Lymphomas are the fifth most common cancer in United States with numerous histological subtypes. Integrating existing clinical information on lymphoma patients provides a platform for understanding biological variability in presentation and treatment response and aids development of novel therapies. We developed a cancer Biomedical Informatics Grid (caBIG) Silver level compliant lymphoma database, called the Lymphoma Enterprise Architecture Data-system (LEAD), which integrates the pathology, pharmacy, laboratory, cancer registry, clinical trials, and clinical data from institutional databases. We utilized the Cancer Common Ontological Representation Environment Software Development Kit (caCORE SDK) provided by National Cancer Institute's Center for Bioinformatics to establish the LEAD platform for data management. The caCORE SDK generated system utilizes an n-tier architecture with open Application Programming Interfaces, controlled vocabularies, and registered metadata to achieve semantic integration across multiple cancer databases. We demonstrated that the data elements and structures within LEAD could be used to manage clinical research data from phase 1 clinical trials, cohort studies, and registry data from the Surveillance Epidemiology and End Results database. This work provides a clear example of how semantic technologies from caBIG can be applied to support a wide range of clinical and research tasks, and integrate data from disparate systems into a single architecture. This illustrates the central importance of caBIG to the management of clinical and biological data.

Keywords: biomedical informatics grid; caCORE SDK; large linked database; non-Hodgkin’s lymphoma; semantic integration.

Figures

Figure 1.
Figure 1.
Layers of semantic interoperability in caBIG™. Semantic interoperability lies in UML model, use of publicly accessible Terminologies/vocabularies/ontologies (EVS–NCI Thesaurus) and use of publicly accessible metadata repository (caDSR).
Figure 2.
Figure 2.
The caCORE workflow. This figure describes the steps involved in creating a silver level compliant system. A UML object model is the input into the workflow. The model is exported from the format native to the tool it was developed into the standard XMI representation. The XMI file is then annotated with terminology services. Once the annotated XMI is reviewed and approved, it is used as input to generate code and public APIs, and it is deposited into production caDSR.
Figure 3.
Figure 3.
Logic Model for lymphoma clinical database developed using Enterprise Architecture. This figure demonstrates the relationships between the key data elements in LEAD™. Components within each key element are not represented in this figure due to practical constraints of resolution and size.
Figure 4.
Figure 4.
Relations between entities and classes from all data sources. This figure depicts the color–coded sources of various key data elements of LEAD™. The codes for colors are shown in the legend. Abbreviations: ELCD, Emory Lymphoma Clinical Data; SEER, Surveillance, Epidemiology, and End Result; CT, Emory University Lymphoma Clinical Trials data.
Figure 5.
Figure 5.
Architecture for LEAD™. This figure describes the architecture of the Lymphoma Enterprise Architecture Data–system. It contains the presentation tier, business tier and data source tier. The web server passes the requests from web browsers and transfers them to the application server which then accesses the backend database and generates the required content dynamically and sends the response back to the web browser through the web server. Outside community accesses the data through the provided programmatic API.
Figure 6.
Figure 6.
Graphical user interface for entering adverse event data into LEAD™. This figure is a sample screen shot of the graphical user interface for entering clinical trial data into LEAD™.

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