The caCORE Software Development Kit: Streamlining construction of interoperable biomedical information services

Abstract

Background: Robust, 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.

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

“…Steps involved in caCORE SDK workflow and the development of LEAD™ are shown in Figure 2 24. The major steps in the workflow include: using case development; information modeling; semantic annotation; metadata registration; code generation; and system deployment 25. LEAD™ development involved creating class diagrams and data models within Enterprise Architecture (EA).…”

Enhanced Semantic Interoperability by Profiling Health Informatics Standards

“…Although UML Profiles for the HL7 HDF and RIM have recently been developed, they have not yet been used for HIS modeling. CaCORE [16] provides an infrastructure to semantically annotate UML information models with specific domain standards and vocabulary, but not exploiting UML profiling mechanisms. The openEHR archetype approach [17] proposes a model-based methodology which uses a proprietary domain-specific language, the Archetype Definition Language (ADL), to represent clinical or other domainspecific concepts by constraining instances of the openEHR information model, but not defining a formal development process nor conforming to the OMG MDA and UML profiling standards.…”

An Application of a Service-oriented System to Support ArrayAnnotation in Custom Chip Design for Epigenomic Analysis

“…These tools are built on the NCI Enterprise Vocabulary Services (EVS) and cancer Data Standards Repository (caDSR) (Covitz, Hartel et al 2003; Phillips, Chilukuri et al 2006), and the Mobius Global Model Exchange (GME) (Hastings, Langella et al 2004) systems. The caDSR and EVS address the need for curation and management of common data types and controlled vocabularies used in cancer research applications.…”

“…Using the UML modeling tool, a set of files containing the UML model, its representation in XML Metadata Interchange (XMI) format, and a human readable report were generated. The XMI file was further annotated using the Semantic Integration Workbench (SIW), which is a toolkit in the caCORE suite of tools(Covitz, Hartel et al 2003; Phillips, Chilukuri et al 2006). The SIW also generates an EVS report, which is reviewed by an EVS expert in the caDSR/ EVS team.…”