OWLing Clinical Data Repositories With the Ontology Web Language

Abstract

BackgroundThe health sciences are based upon information. Clinical information is usually stored and managed by physicians with precarious tools, such as spreadsheets. The biomedical domain is more complex than other domains that have adopted information and communication technologies as pervasive business tools. Moreover, medicine continuously changes its corpus of knowledge because of new discoveries and the rearrangements in the relationships among concepts. This scenario makes it especially difficult to offer good tools to answer the professional needs of researchers and constitutes a barrier that needs innovation to discover useful solutions.ObjectiveThe objective was to design and implement a framework for the development of clinical data repositories, capable of facing the continuous change in the biomedicine domain and minimizing the technical knowledge required from final users.MethodsWe combined knowledge management tools and methodologies with relational technology. We present an ontology-based approach that is flexible and efficient for dealing with complexity and change, integrated with a solid relational storage and a Web graphical user interface.ResultsOnto Clinical Research Forms (OntoCRF) is a framework for the definition, modeling, and instantiation of data repositories. It does not need any database design or programming. All required information to define a new project is explicitly stated in ontologies. Moreover, the user interface is built automatically on the fly as Web pages, whereas data are stored in a generic repository. This allows for immediate deployment and population of the database as well as instant online availability of any modification.ConclusionsOntoCRF is a complete framework to build data repositories with a solid relational storage. Driven by ontologies, OntoCRF is more flexible and efficient to deal with complexity and change than traditional systems and does not require very skilled technical people facilitating the engineering of clinical software systems.

OntoCR: A CEN/ISO-13606 clinical repository based on ontologies

“…Evaluations of OntoCRF [23] showed a linear behavior when uploading and downloading the entire ontology. User interaction with the system in other projects using OntoCRF seems no different than with other systems.…”

“…This approach is called OntoCRF [23]. In OntoCRF, the repository is independent of content specification.…”

An Electronic Healthcare Record Server Implemented in PostgreSQL

“…This has been formalised in the current version as the "Pattern", literally a model for collections of Java annotation-like [26] statements from which an application can be derived. Healthcare applications lend themselves to Model-Driven Development and for example, OntoCRF [27] is also model-driven; this time grounded in the Web Ontology Language and targeted initially at research.…”

An ontology‐based clinical data warehouse for scientific research

“…Here again, the purpose is to find a superior common data model to compare data of different medical institutions. The most comparable work was published in 2014 by [13] Lozano et al, who also present an ontology-based system, called OWLing. Their intention is comparable to the abovementioned, but their implementation is completely based upon the web ontology-language OWL.…”