Description

Academic Lecture by Ali Raza - Software Developer in the Bio-Ontology Research Group at KAUST Computational Bioscience Research Center (CBRC), Maxat Kulmanov - Ph.D. Candidate in the Bio-Ontology Research Group at KAUT CBRC, Nasser Mohiuddin - Research Data Storage Specialist working with Systems, Storage and Automation Team (SSAT) group at KAUST IT, and Zulfikhar Mohammed - Systems Specialist at KAUST. 

ABOUT THIS EVENT

With the recent large scale prevalence of micro-sensors and devices to measure medical data, there is an exponential growth in data of individuals’ health and bodily functions.  To properly store, access, and make sense of this humongous amount of data needs powerful tools.  Elastic Search is one such tool which enables the interpreting and presenting of big data in an orderly manner.  Using Elastic Search on medical data will not only empower doctors to quickly scan and utilize the patients’ biological data but will give the necessary information and guidance to the patients themselves to administer pre-programmed, remedial actions to rectify their health situation to a much greater extent than currently possible.

This lecture will make users aware of the powerful search and display capabilities of Elastic Search. It will demonstrate how the bulk data on individuals’ health statistics being collected can be channeled to common storage (database) and then processed in an intelligent manner to yield results that can be seen and understood by the common man. It will produce personalized results that will inspire users to take an active interest in managing their health issues, using various vital statistics like blood pressure, heart rate, body temperature, metabolism, etc.

The participants will need to have an interest in biomedical applications and a keen interest in working with and mining large amounts of data.  While no prerequisites are imposed to attend, spectators are expected to come with a keen sense of learning a new concept applied to real-life problems.

This two-hour event will be divided into two sessions:

• The first session will be presented by IT (Information Technology).
• The second session will be presented by the Bio-Ontology Research Group (BORG) under the Computational Bioscience Research Center (CBRC) department.

The session by IT will give an overall presentation of Elastic Search, its basic workings, its data-storing structure, and its search capabilities.  During this session, an important topic of discussion and demonstration will be to trigger alarms and suggest actions based on pre-set thresholds of the data being received.  If those thresholds are crossed, then the system will suggest actions to the patients which are pre-programmed by health professionals.  The data thus obtained can also be plotted over time to display the progress or regress of the health of the individual.

These concepts will be demonstrated and displayed by using sample data, the process to query that data will be shown and graphs will be visualized.

During the second session presented by the BORG researchers, the discussion will consist of two use-cases being currently researched by the group at KAUST.

1. AberOWL is a framework for ontology-based access to biological data. It consists of a repository of bio-ontologies, a set of web services that provide access to OWL(-EL) reasoning over the ontologies, and several frontends that utilize the ontology repository and reasoning services to provide access to specific biological datasets. It uses Elastic Search to index metadata of the ontology classes.

2. Bio2Vec is a platform that enables the development of machine learning and data analytics methods to be applied to biological Big Data, with the aim of discovering molecular mechanisms underlying complex disease and drugs’ mode of action. It covers embeddings from text and knowledge graphs such as GO terms, proteins, drugs, diseases, proteins and protein interactions. Bio2Vec provides FAIR (Findable, Accessible, Interoperable and Reusable) data, eliminating the need for data preparation for data consumers and web service design for data providers. It uses Elastic Search to index embeddings and their metadata.

Overall, the participants will walk away from this workshop conversant with the ways in which Elastic Search can be used and configured to produce customizable and personalized scores, charts and graphs.  With active interaction and participation from the audience, the workshop will pique the curiosity of the users to play an active role in taking care of their own well-being while assisting doctors to analyze and arrive at a more accurate diagnosis of their conditions through the use of Elastic Search to derive personalized medical results.

From the second session, the participants will see the practical application of Elastic Search being used by one of our own KAUST academic departments to solve real-life research problems.  This will enrich their knowledge of the utility of this powerful tool.

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