Abstract
BackgroundRobust, programmatically accessible biomedical information services that syntactically and semantically interoperate with other resources are challenging to construct. Such systems require the adoption of common information models, data representations and terminology standards as well as documented application programming interfaces (APIs). The National Cancer Institute (NCI) developed the cancer common ontologic representation environment (caCORE) to provide the infrastructure necessary to achieve interoperability across the systems it develops or sponsors. The caCORE Software Development Kit (SDK) was designed to provide developers both within and outside the NCI with the tools needed to construct such interoperable software systems.ResultsThe caCORE SDK requires a Unified Modeling Language (UML) tool to begin the development workflow with the construction of a domain information model in the form of a UML Class Diagram. Models are annotated with concepts and definitions from a description logic terminology source using the Semantic Connector component. The annotated model is registered in the Cancer Data Standards Repository (caDSR) using the UML Loader component. System software is automatically generated using the Codegen component, which produces middleware that runs on an application server. The caCORE SDK was initially tested and validated using a seven-class UML model, and has been used to generate the caCORE production system, which includes models with dozens of classes. The deployed system supports access through object-oriented APIs with consistent syntax for retrieval of any type of data object across all classes in the original UML model. The caCORE SDK is currently being used by several development teams, including by participants in the cancer biomedical informatics grid (caBIG) program, to create compatible data services. caBIG compatibility standards are based upon caCORE resources, and thus the caCORE SDK has emerged as a key enabling technology for caBIG.ConclusionThe caCORE SDK substantially lowers the barrier to implementing systems that are syntactically and semantically interoperable by providing workflow and automation tools that standardize and expedite modeling, development, and deployment. It has gained acceptance among developers in the caBIG program, and is expected to provide a common mechanism for creating data service nodes on the data grid that is under development.
Highlights
Robust, programmatically accessible biomedical information services that syntactically and semantically interoperate with other resources are challenging to construct
Systems developed using the cancer common ontologic representation environment (caCORE) methodology use the same approach to defining, registering, and adopting data and representation standards. Clients of those systems can draw upon multiple sources using similar application programming interfaces (APIs) calls, and can rely on semantic equivalence of the data retrieved. caCORE consists of several components
Usage of the Software Development Kit (SDK) follows a particular workflow pattern that mirrors our approach to constructing caCORE-type resources
Summary
Programmatically accessible biomedical information services that syntactically and semantically interoperate with other resources are challenging to construct Such systems require the adoption of common information models, data representations and terminology standards as well as documented application programming interfaces (APIs). Systems developed using the caCORE methodology use the same approach to defining, registering, and adopting data and representation standards. A number of biomedical informatics groups use caCORE for the management of data standards and to create interoperable genomic, translational, and clinical research applications. Examples of such applications include the Cancer Models Database[4], caWorkbench[5], Cancer Molecular Analysis Project[6], and Cancer Centralized Clinical Database[7]
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