In this dissertation, we present a novel approach for Web service mining. Web service mining is a new research discipline. It is different from conventional top down service composition approaches that are driven by specific search criteria. Web service mining starts with no such criteria and aims at the discovery of interesting and useful compositions of existing Web services. Web service mining requires the study of three main research topics: semantic description of Web services, efficient bottom up composition of composable services, and interestingness and usefulness evaluation of composed services. We first propose a Web service ontology to describe and organize the constructs of a Web service. We introduce the concept of Web service operation interface for the description of shared Web service capabilities and use Web service domains for grouping Web service capabilities based on these interfaces. We take clues from how Nature solves the problem of molecular composition and introduce the notion of Web service recognition to help devise efficient bottom up service composition strategies. We introduce several service recognition mechanisms that take advantage of the domain-based categorization of Web service capabilities and ontology-based description of operation semantics. We take clues from the drug discovery process and propose a Web service mining framework to group relevant mining activities into a progression of phases that would lead to the eventual discovery of useful compositions. Based on the composition strategies that are derived from recognition mechanisms, we propose a set of algorithms in the screening phase of the framework to automatically identify leads of service compositions. We propose objective interestingness and usefulness measures in the evaluation phase to narrow down the pool of composition leads for further exploration. To demonstrate the effectiveness of our framework and to address challenges faced by existing biological data representation methodologies, we have applied relevant techniques presented in this dissertation to the field of biological pathway discovery. / Ph. D.

Single Nucleotide Polymorphisms (SNPs) are the most frequent genomic variations and the main basis for genetic differences among individuals and many diseases. As genotyping millions of SNPs at once is now possible with the microarrays and advanced sequencing technologies, SNPs are becoming more popular as genomic biomarkers. Like other high-throughput research techniques, genome wide association studies (GWAS) of SNPs usually hit a bottleneck after statistical analysis of significantly associated SNPs, as there is no standardized approach to prioritize SNPs or to select representative SNPs that show association with the conditions under study. In this study, a java based integrated system that makes use of major public databases to prioritize SNPs according to their biological relevance and statistical significance has been constructed. The Analytic Hierarchy Process, has been utilized for objective prioritization of SNPs and a new emerging methodology for second-wave analysis of genes and pathways related to disease associated SNPs based on a combined p-value approach is applied into the prioritization scheme. Using the subset of SNPs that is most representative of all SNPs associated with the diseases reduces the required computational power for analysis and decreases cost of following association and biomarker discovery studies. In addition to the proposed prioritization system, we have developed a novel feature selection method based on Simulated Annealing (SA) for representative SNP selection. The validity and accuracy of developed model has been tested on real life case control data set and produced biologically meaningful results. The integrated desktop application developed in our study will facilitate reliable identification of SNPs that are involved in the etiology of complex diseases, ultimately supporting timely identification of genomic disease biomarkers, and development of personalized medicine approaches and targeted drug discoveries.