Over the past thirty years, clinical research has benefited substantially from the adoption of electronic medical record systems. As deployment has increased, so too has the number of researchers seeking to improve the overall analytical environment by way of tools and models. Although much work has been done, there are still many uninvestigated areas; two of which are explored in this dissertation. The first pertains to the physical storage of the data itself. There are two generally accepted storage models: relational and entity-attribute-value (EAV). For clinical data, EAV systems are preferred due to their natural way of managing many-to-many relationships, sparse attributes, and dynamic processes along with minimal conversion effort and reduction in federation complexities. However, the relational database management systems on which they are implemented, are not intended to organize and retrieve data in this format; eroding their performance gains. To combat this effect, we present the foundation for an EAV Database Management System (EDBMS). We discuss data conversion methodologies, formulate the requisite metadata and partitioned type-sensing index structures, and provide detailed runtime and experimental analysis with five extant methods. Our results show that the prototype, EAVDB, reduces space and conversion requirements while enhancing overall query performance. The second topic concerns query performance in a federated environment. One method used to decrease query execution time, is to pre-compute and store "beneficial" queries (views). The View Selection Problem (VSP) identifies these views subject to resource constraints. A federated model, however, has yet to be developed. In this dissertation, we submit three advances in view materialization. First, a more robust optimization function, the Minimum-Maintenance View Selection Problem (MMVSP), is derived by combining existing approaches. Second, the Federated View Selection Problem (FVSP), built upon the MMVSP, and federated data cube lattice are formalized. The FVSP allows for multiple querying nodes, partial and full materialization, and data propagation constriction. The latter two are shown to greatly reduce the overall number of valid solutions within the solution space and thus a novel, multi-tiered approach is given. Lastly, EAV materialization, which is introduced in this dissertation, is incorporated into an expanded, multi-modal variant of the FVSP. As models and heuristics for both the federated and EAV VSP, to the best of our knowledge, do not exist, this research defines two new branches of data warehouse optimization. Coupled with our EDBMS design, this dissertation confronts two main challenges associated with clinical data warehousing and federation.

Clinical study data is usually collected without knowing what kind of data is going to be collected in advance. In addition, all of the possible data points that can apply to a patient in any given clinical study is almost always a superset of the data points that are actually recorded for a given patient. As a result of this, clinical data resembles a set of sparse data with an evolving data schema. To help researchers at the Moffitt Cancer Center better manage clinical data, a tool was developed called GURU that uses the Entity Attribute Value model to handle sparse data and allow users to manage a database entity’s attributes without any changes to the database table definition. The Entity Attribute Value model’s read performance gets faster as the data gets sparser but it was observed to perform many times worse than a wide table if the attribute count is not sufficiently large. Ultimately, the design trades read performance for flexibility in the data schema.

Creating a database to manage medical data is not the easiest. We create a database to be used for a presentation tool that presents medical data about patients that is stored in the database. We examine which of the three databases, MySQL with relational design, MySQL with EAV design and MongoDB that are best suited for storing medical data. The analysis i performed in two steps. The first step handles the database that is most effective to retriev data. The second step examines how easy it is to change the structure of the various databases. The results show that depending on whether efficiency or maintenance is most important, different databases are the best choise. MySQL with relational design proves to be most effective while MongoDB is the easiest to maintain.

This thesis describes the problems of storage and management of biological data, particularly of Haloalkane Dehalogenase enzymes. Furthermore, the thesis aims at project HADES (HAloalkane DEhalogenase databaSe) initiated by protein engineering group of Loschmidt Laboratories, Masaryk University in Brno. This is a project whose main goal is simply to store, preserve and display a wide variety of proteins data. The result of this work is a flexible database system allowing easy extensibility and maintainability, which is built on technologies Apache, PostgreSQL and PHP using the Zend Framework.