Patient medical records are a valuable resource that can be used for many purposes including managing and planning for future health needs as well as clinical research. Health databases such as the clinical practice research datalink (CPRD) and many other similar initiatives can provide researchers with a useful data source on which they can test their medical hypotheses. However, this can only be the case when researchers have a good set of hypotheses to test on the data. Conversely, the data may have other equally important areas that remain unexplored. There is a chance that some important signals in the data could be missed. Therefore, further analysis is required to make such hidden areas become more obvious and attainable for future exploration and investigation.Data mining techniques can be effective tools in discovering patterns and signals in large-scale patient data sets. These techniques have been widely applied to different areas in medical domain. Therefore, analysing patient data using such techniques has the potential to explore the data and to provide a better understanding of the information in patient records. However, the heterogeneity and complexity of medical data can be an obstacle in applying data mining techniques. Much of the potential value of this data therefore goes untapped.This thesis describes a novel methodology that reduces the dimensionality of primary care data, to make it more amenable to visualisation, mining and clustering. The methodology involves employing a combination of ontology-based semantic similarity and principal component analysis (PCA) to map the data into an appropriate and informative low dimensional space. The aim of this thesis is to develop a novel methodology that provides a visualisation of patient records. This visualisation provides a systematic method that allows the formulation of new and testable hypotheses which can be fed to researchers to carry out the subsequent phases of research. In a small-scale study based on Salford Integrated Record (SIR) data, I have demonstrated that this mapping provides informative views of patient phenotypes across a population and allows the construction of clusters of patients sharing common diagnosis and treatments.The next phase of the research was to develop this methodology and explore its application using larger patient cohorts. This data contains more precise relationships between features than small-scale data. It also leads to the understanding of distinct population patterns and extracting common features. For such reasons, I applied the mapping methodology to patient records from the CPRD database. The study data set consisted of anonymised patient records for a population of 2.7 million patients. The work done in this analysis shows that methodology scales as O(n) in ways that did not require large computing resources. The low dimensional visualisation of high dimensional patient data allowed the identification of different subpopulations of patients across the study data set, where each subpopulation consisted of patients sharing similar characteristics such as age, gender and certain types of diseases.A key finding of this research is the wealth of data that can be produced. In the first use case of looking at the stratification of patients with falls, the methodology gave important hypotheses; however, this work has barely scratched the surface of how this mapping could be used. It opens up the possibility of applying a wide range of data mining strategies that have not yet been explored. What the thesis has shown is one strategy that works, but there could be many more. Furthermore, there is no aspect of the implementation of this methodology that restricts it to medical data. The same methodology could equally be applied to the analysis and visualisation of many other sources of data that are described using terms from taxonomies or ontologies.