Design patterns for the development of electronic health record-driven phenotype extraction algorithms

AbstractBackgroundDesign patterns, in the context of software development and ontologies, provide generalized approaches and guidance to solving commonly occurring problems, or addressing common situations typically informed by intuition, heuristics and experience. While the biomedical literature contains broad coverage of specific phenotype algorithm implementations, no work to date has attempted to generalize common approaches into design patterns, which may then be distributed to the informatics community to efficiently develop more accurate phenotype algorithms.MethodsUsing phenotyping algorithms stored in the Phenotype KnowledgeBase (PheKB), we conducted an independent iterative review to identify recurrent elements within the algorithm definitions. We extracted and generalized recurrent elements in these algorithms into candidate patterns. The authors then assessed the candidate patterns for validity by group consensus, and annotated them with attributes.ResultsA total of 24 electronic Medical Records and Genomics (eMERGE) phenotypes available in PheKB as of 1/25/2013 were downloaded and reviewed. From these, a total of 21 phenotyping patterns were identified, which are available as an online data supplement.ConclusionsRepeatable patterns within phenotyping algorithms exist, and when codified and cataloged may help to educate both experienced and novice algorithm developers. The dissemination and application of these patterns has the potential to decrease the time to develop algorithms, while improving portability and accuracy

SecMVC : a model for secure software design based on the model-view-controller pattern

Current advances in the software development industry are growing more ubiquitous by the day. This has caused for security, not only in the broader sense, but specifically within the design and overall development of software itself, to become all the more important. An evidently prevalent problem in the domain of software development is that software security is not consistently addressed during design, which undermines core security concerns, and leads to the development of insecure software. This research seeks to address this issue via a model for secure software design, which is based on a software design pattern, namely, the Model-View-Controller (MVC) pattern. The use of a pattern to convey knowledge is not a new notion. However, the ability of software design patterns to convey secure software design is an idea worth investigating. Following identification of secure software design principles and concepts, as well as software design patterns, specifically those relating to the MVC pattern, a model was designed and developed. With the MVC pattern argued as being a suitable foundation for the model, the security conscious MVC (SecMVC) combines secure software design principles and concepts into the MVC pattern. Together herewith, the MVC pattern’s components in the MVC Compound pattern, namely: the Observer pattern, the Strategy pattern, and the Composite pattern, have provided further sub-models for less abstraction and greater detail. These sub-models were developed, as a result of the SecMVC model’s evaluation in the validation for this study, an expert review. Argued in the light of similar research methods, the expert review was chosen – along with a process that included the use of two expert participants to validate the SecMVC model. It was determined through the expert review that the SecMVC model is of sufficient utility, quality, and efficacy to constitute research value. The research methodology process followed was design science, in which the SecMVC model, which includes its related sub-models, serves as the artefact and research output of this study. This research study contributes evidence of the feasibility for integrating knowledge into software design patterns. This includes the SecMVC model itself. In addition, it argues for the use of an expert review, as an evaluative research method for such an artifact

Closing the gap between guidance and practice, an investigation of the relevance of design guidance to practitioners using object-oriented technologies

This thesis investigates if object oriented guidance is relevant in practice, and how this affects software that is produced. This is achieved by surveying practitioners and studying how constructs such as interfaces and inheritance are used in open-source systems. Surveyed practitioners framed 'good design' in terms of impact on development and maintenance. Recognition of quality requires practitioner judgement (individually and as a group), and principles are valued over rules. Time constraints heighten sensitivity to the rework cost of poor design decisions. Examination of open source systems highlights the use of interface and inheritance. There is some evidence of 'textbook' use of these structures, and much use is simple. Outliers are widespread indicating a pragmatic approach. Design is found to reflect the pressures of practice - high-level decisions justify 'designed' structures and architecture, while uncertainty leads to deferred design decisions - simpler structures, repetition, and unconsolidated design. Sub-populations of structures can be identified which may represent common trade-offs. Useful insights are gained into practitioner attitude to design guidance. Patterns of use and structure are identified which may aid in assessment and comprehension of object oriented systems.This thesis investigates if object oriented guidance is relevant in practice, and how this affects software that is produced. This is achieved by surveying practitioners and studying how constructs such as interfaces and inheritance are used in open-source systems. Surveyed practitioners framed 'good design' in terms of impact on development and maintenance. Recognition of quality requires practitioner judgement (individually and as a group), and principles are valued over rules. Time constraints heighten sensitivity to the rework cost of poor design decisions. Examination of open source systems highlights the use of interface and inheritance. There is some evidence of 'textbook' use of these structures, and much use is simple. Outliers are widespread indicating a pragmatic approach. Design is found to reflect the pressures of practice - high-level decisions justify 'designed' structures and architecture, while uncertainty leads to deferred design decisions - simpler structures, repetition, and unconsolidated design. Sub-populations of structures can be identified which may represent common trade-offs. Useful insights are gained into practitioner attitude to design guidance. Patterns of use and structure are identified which may aid in assessment and comprehension of object oriented systems