Linked Open Data Alignment & Querying.The recent emergence of the Linked Data approach for publishing data represents a major step forward in realizing the original vision of a web that can "understand and satisfy the requests of people and machines to use the web content" i.e. the Semantic Web. This new approach has resulted in the Linked Open Data (LOD) Cloud, which includes more than 295 large datasets contributed by experts belonging to diverse communities such as geography, entertainment, and life sciences. However, the current interlinks between datasets in the LOD Cloud as we will illustrate are too shallow to realize much of the benefits promised. If this limitation is left unaddressed, then the LOD Cloud will merely be more data that suffers from the same kinds of problems, which plague the Web of Documents, and hence the vision of the Semantic Web will fall short.This thesis presents a comprehensive solution to address the issue of alignment and relationship identification using a bootstrapping based approach. By alignment we mean the process of determining correspondences between classes and properties of ontologies. We identify subsumption, equivalence and part-of relationship between classes. The work identifies part-of relationship between instances. Between properties we will establish subsumption and equivalence relationship. By bootstrapping we mean the process of being able to utilize the information which is contained within the datasets for improving the data within them. The work showcases use of bootstrapping based methods to identify and create richer relationships between LOD datasets. The BLOOMS project (http://wiki.knoesis.org/index.php/BLOOMS) and the PLATO project, both built as part of this research, have provided evidence to the feasibility and the applicability of the solution.