IntroductionWithin the advancements in information and communication technologies in the last years, there are two significant trends. First, the number, usage and capabilities of the end-user devices, such as smartphones, tablets, wearables, and sensors, are continually increasing. Second, end-user devices are becoming more and more connected to each other and the Internet. With the advent of 5G networks, the vision of ubiquitous connected physical objects, commonly referred to as the Internet of Things (IoT), has become a reality. In the world of connected physical devices, there is a massive influx of data, which is valuable for both real-time as well as historical analysis. Analysis of the generated data in real-time is gaining prominence. Such analysis can lead to valuable insights regarding individual preferences, group preferences and patterns of end-users (e.g. mobility models), the state of engineering structures (e.g. as in structural health monitoring) and the future state of the physical environment (e.g. flood prediction in rivers). These insights can, in turn, allow the creation of sophisticated, AbstractIncreased sensing data in the context of the Internet of Things (IoT) necessitates data analytics. It is challenging to write applications for Big Data systems due to complex, highly parallel software frameworks and systems. The inherent complexity in programming Big Data applications is also due to the presence of a wide range of target frameworks, with different data abstractions and APIs. The paper aims to reduce this complexity and its ensued learning curve by enabling domain experts, that are not necessarily skilled Big Data programmers, to develop data analytics applications via domain-specific graphical tools. The approach follows the flow-based programming paradigm used in IoT mashup tools. The paper contributes to these aspects by (i) providing a thorough analysis and classification of the widely used Spark framework and selecting suitable data abstractions and APIs for use in a graphical flow-based programming paradigm and (ii) devising a novel, generic approach for programming Spark from graphical flows that comprises early-stage validation and code generation of Spark applications. Use cases for Spark have been prototyped and evaluated to demonstrate code-abstraction, automatic data abstraction interconversion and automatic generation of target Spark programs, which are the keys to lower the complexity and its ensued learning curve involved in the development of Big Data applications.
Background Modern data-driven medical research provides new insights into the development and course of diseases and enables novel methods of clinical decision support. Clinical and translational data warehouses, such as Informatics for Integrating Biology and the Bedside (i2b2) and tranSMART, are important infrastructure components that provide users with unified access to the large heterogeneous data sets needed to realize this and support use cases such as cohort selection, hypothesis generation, and ad hoc data analysis. Objective Often, different warehousing platforms are needed to support different use cases and different types of data. Moreover, to achieve an optimal data representation within the target systems, specific domain knowledge is needed when designing data-loading processes. Consequently, informaticians need to work closely with clinicians and researchers in short iterations. This is a challenging task as installing and maintaining warehousing platforms can be complex and time consuming. Furthermore, data loading typically requires significant effort in terms of data preprocessing, cleansing, and restructuring. The platform described in this study aims to address these challenges. Methods We formulated system requirements to achieve agility in terms of platform management and data loading. The derived system architecture includes a cloud infrastructure with unified management interfaces for multiple warehouse platforms and a data-loading pipeline with a declarative configuration paradigm and meta-loading approach. The latter compiles data and configuration files into forms required by existing loading tools, thereby automating a wide range of data restructuring and cleansing tasks. We demonstrated the fulfillment of the requirements and the originality of our approach by an experimental evaluation and a comparison with previous work. Results The platform supports both i2b2 and tranSMART with built-in security. Our experiments showed that the loading pipeline accepts input data that cannot be loaded with existing tools without preprocessing. Moreover, it lowered efforts significantly, reducing the size of configuration files required by factors of up to 22 for tranSMART and 1135 for i2b2. The time required to perform the compilation process was roughly equivalent to the time required for actual data loading. Comparison with other tools showed that our solution was the only tool fulfilling all requirements. Conclusions Our platform significantly reduces the efforts required for managing clinical and translational warehouses and for loading data in various formats and structures, such as complex entity-attribute-value structures often found in laboratory data. Moreover, it facilitates the iterative refinement of data representations in the target platforms, as the required configuration files are very compact. The quantitative measurements presented are consistent with our experiences of significantly reduced efforts for building warehousing platforms in close cooperation with medical researchers. Both the cloud-based hosting infrastructure and the data-loading pipeline are available to the community as open source software with comprehensive documentation.
scite is a Brooklyn-based organization that helps researchers better discover and understand research articles through Smart Citations–citations that display the context of the citation and describe whether the article provides supporting or contrasting evidence. scite is used by students and researchers from around the world and is funded in part by the National Science Foundation and the National Institute on Drug Abuse of the National Institutes of Health.
hi@scite.ai
10624 S. Eastern Ave., Ste. A-614
Henderson, NV 89052, USA
Copyright © 2024 scite LLC. All rights reserved.
Made with 💙 for researchers
Part of the Research Solutions Family.