Submitted to the faculty of Indiana University in partial fulfillment of the requirements for the degree Masters of Science in the School of Informatics Indiana University December 2005 / This project addresses the need for an increased expressivity and robustness of ontologies already supporting BACIIS and SIBIOS, two systems for data and service integration in the life sciences. The previous ontology solutions as global schema and facilitator of service discovery sustained the purposes for which they were built to provide, but were in need of updating in order to keep up with more recent standards in ontology descriptions and utilization as well as increase the breadth of the domain and expressivity of the content. Thus, several tasks were undertaken to increase the worth of the system ontologies. These include an upgrade to a more recent ontology language standard, increased domain coverage, and increased expressivity via additions of relationships and hierarchies within the ontology as well as increased ease of maintenance by a distributed design.

Submitted to the Faculty of the School of Informatics in parial fulfillment of the requirements for the degree of Master of Schience in Bioinformatics Indiana University August 2006 / Decoding the human genome resulted in generating large amount of data that need to be analyzed and given a biological meaning. The field of Life Schiences is highly information driven. The genomic data are mainly the gene expression data that are obtained from measurement of mRNA levels in an organism. Efficiently processing large amount of gene expression data has been possible with the help of high throughput technology. Research studies working on microarray data has led to the possibility of finding disease biomarkers. Carrying out biomarker discovery experiments has been greatly facilitated with the emergence of various analytical and visualization tools as well as annotation databases. These tools and databases are often termed as 'bioinformatics services'. The main purpose of this research was to develop SIBIOS (Bystem for Integration of Bioinformatics Services) as a platform to carry out microarray experiments for the purpose of biomarker discovery. Such experiments require the understanding of the current procedures adopted by researchers to extract biologically significant genes. In the course of this study, sample protocols were built for the purpose of biomarker discovery. A case study on the BCR-ABL subtype of ALL was selected to validate the results. Different approaches for biomarker discovery were explored and both statistical and mining techniques were considered. Biological annotation of the results was also carried out. The final task was to incorporate the new proposed sample protocols into SIBIOS by providing the workflow capabilities and therefore enhancing the system's characteristics to be able to support biomarker discovery workflows.