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2003-2004 Success Stories

BioMiner

In Brief

This past year, NRC-IIT’s BioMiner technology has grown into a successful platform for several key initiatives. An integrated data mining infrastructure to process and analyze vast amounts of information captured in the study of genes and protein functions, the technology is a key contributor to current research in genomics and proteomics. The project has united research groups within the Institute, across the NRC, and from research centres abroad to develop new and innovative approaches for capturing knowledge from data. The project is exemplary of NRC’s partnership philosophy and it represents NRC-IIT’s strategic directions, as well as a more integrated approach to research. Most importantly, the project is playing an important role in the advancement of health care by providing tools that will potentially result in the enhanced diagnosis and treatment of disease.

“The software tools developed during the Biomine project are also beginning to attract the attention of potential clients even though overt attempts to commercialize the technology have not yet been initiated. The eventual commercialization of these tools will be of major benefit to other scientists not just in Canada but world-wide.” -- Dr. Danica Stanimirovic, Director, Neurobiology Program, Institute for Biological Sciences

The BioMiner Infrastructure

The BioMiner Infrastructure was the result of the BioMine project, established in August 1999 to respond to the need of researchers at the NRC-Institute for Biological Sciences (NRC-IBS) for a tool capable of processing biochip data in order to study gene and protein function. With approximately 20,000 genes per chip, plus the vast amounts of data resulting from technological advancement in recent years, no existing tools could meet NRC-IBS’ requirements for efficient and accurate processing and analysis.

As a result, in collaboration with NRC-IBS, NRC-IIT began to investigate genomics data mining requirements and existing data mining tools and techniques. Having discovered there was no existing tool that could meet all of the BioChip data mining requirements, NRC-IIT developed BioMiner, an integrated system to process and analyze several types of genomics and proteomics data. BioMiner fulfills three important primary tasks: identifying all essential data characteristics through data pre-processing techniques, discovering meaningful relationships between cases/objects, and discriminating and distinguishing objects of different classes. The tool plays a vital role in determining gene functions and in monitoring how genes respond to a certain process. It identifies the reactions of proteins to the presence of other proteins and drug compounds, indicating its strong potential in the area of drug discovery. Most recently, the tool has been equipped with the ability to find biological sequence motif patterns in humans, yeast and vertebrates, enabling the discovery of small structural elements called transcription factor (TF) binding sites recognizable in several proteins. The TF activates or suppresses the first step in a gene’s expression. This new function will provide researchers with a heightened understanding of gene expression.

BioMiner has enabled NRC-IIT to contribute to NRC’s Genomics in Health Initiative and to partner with the NRC’s Institutes for Biological Studies, Biotechnology Research and Plant Biotechnology, offering them the use of BioMiner to analyze the genomic and proteomic data they produce. In return, they provide feedback on BioMiner’s functionalities and system design. Case studies employing BioMiner include: Gene Expression Analysis in Neurogenesis (NRC-IBS), Analysis of Regulatory Gene Expression Networks (NRC- IBS), Gene Identification for Alzheimer’s Disease (NRC-IBS), Gene Response Analysis for Plant Disease (NRC-PBI), Gene Identification in Mammary Cells (with NRC-BRI) and Disease Modeling in Hepatitis C Virus Transgenic Mice (CHEO and NRC-IBS). The tool has enabled researchers in the latter project to make significant advances in their field of investigation.

As Dr. Marko Kryworuchko, Scientist at the Division of Virology, CHEO – Research Institute explains, “The Biominer software platform and the interaction of our multi-disciplinary teams will continue to be invaluable for the processing, analysis and interpretation of the massive amount and complexity of the resulting data […] The approach we are taking will continue to generate a wealth of data and is expected to identify potentially new drug targets and important markers to evaluate the efficacy of therapeutics and our vaccine candidates.”

Gene Identification for Alzheimer’s Disease also provided very encouraging results. It was able to identify 67 genes associated with the disease, while previously only 17 genes had been linked to it. These improved results increase the capacity for disease modeling, which in turn will speed the discovery of effective treatments and possible cures.

Building on BioMiner’s current capabilities, NRC-IIT is proposing a new BioIntegrator project to create a new and more powerful tool for genomic and proteomic research. This project would integrate Litminer, a text mining tool developed by NRC-IIT’s Interactive Information group, and BioMiner, in order to also capture important text-based data in scientific literature. This integration would enable the recording of all previous related experiments and investigations and could serve as a cross-validation mechanism for research results in each respective area. The initial proposal is to focus primarily on the identification of genes and how they relate to particular groups of diseases and genes associated with possible drug targets in the functional networks. However, these tools could also be adapted for use across many areas of scientific research. This multi-disciplinary initiative, therefore, is also a strong reflection of NRC-IIT’s move towards developing more cross-group synergies within the Institute. This new outgrowth of BioMiner will also stand in good stead for its partnership with GHI, as well as its new joint venture to design a comprehensive Biointelligence system.

Currently working towards that goal through a joint venture established this year with Spain’s Ministerio de Ciencia Tecnología (Ministry of Science and Technology - MCYT), CNB (Centro Nacional de Biotecnología) Madrid, CNIO (Centro Nacional de Investigaciones Oncológicas) Madrid, NRC-Institute for Biological Sciences, NRC-Biotechnology Research Institute and the Children’s Hospital of Eastern Ontario, research activities are presently focused on integrating genomics and proteomics, automated knowledge discovery in genomics and identification of gene regulatory networks using time series data. This new Biointelligence direction, which overlaps with the principles of artificial intelligence and knowledge-based systems, requires extensive research in automated data mining, as well as an understanding of key issues in intelligent decision support systems. It also involves structuring and disseminating knowledge discovered from genomics applications, and its integration with other forms of knowledge, such as clinical documents and patient information readily available from medical organizations, labs or pharmaceutical companies. This ambitious project would employ NRC-IIT’s BioMiner software to enable the generation and analysis of large volumes of laboratory and clinical data and provide support for improved disease classification, diagnosis and therapy. Through this project, BioMiner could potentially play a vital role in areas such as pathology and laboratory medicine. It could also advance the field of pharmocogenomics, leading to the development of drugs tailored specifically to an individual’s genetic makeup, and toxicogenomics, advancing knowledge of how the genome is involved in response to environmental stressors and toxicants.

Contact

Dr. Abolfazl Famili (Fazel)
Research Officer
Integrated Reasoning
NRC Institute for Information Technology
1200 Montreal Road
Building M-50, Room 368
Ottawa, ON K1A 0R6
Telephone: +1 (613) 993-8554
Fax: +1 (613) 952-0215
E-mail: Fazel.Famili@nrc-cnrc.gc.ca