2013 Archived Content
Fifth Annual

Integrated R&D Informatics and Knowledge Management

Leveraging IT and Informatics to Enable Global Information Sharing


Day 1Day 2 | Day 3

Friday, February 15

8:00 am Morning Coffee


Data Integration Strategies to Support
Clinical & Translational Research

8:30 Chairperson's Remarks

Ajay Shah, Ph.D., Director, Research Informatics Division, City of Hope

8:35 Translational Research Informatics Platform at City of Hope

Ajay Shah, Ph.D., Director, Research Informatics Division, City of Hope

City of Hope (COH) is implementing several components of its Translational Research Informatics Platform. This platform leverages COH Enterprise Data Warehouse. Natural language processing components of the platform allows for analysis of electronic medical health records, and extraction of coded fields from these records. The computational analysis components of the platform incorporates machine learning techniques. The platform leverages terminologies from UMLS and integrates with Open Source tools e.g., i2b2, R etc. and commercial solutions including Pipeline Pilot.

9:05 Path to Develop Integrated Data for Biomarker Research

Carol Bova Hill, Ph.D., Informatics Project Leader II, Clinical Research Informatics, Duke Clinical Research Institute

Integration of data to support translational research requires rigorous understanding of data and highlights the crucial role of the Informaticist.I will outline efforts and challenges to create a robust systematic environment to support the utilization of biospecimens at DCRI.

9:35 Data Visualization in Clinical Research

Dimitris Agrafiotis, Janssen R&D, Johnson & Johnson

Data visualization is a powerful analytic technique that can greatly enhance the efficiency and quality of the clinical monitoring process by enabling visual detection of emerging safety trends, identification of outliers and data quality issues, evaluation of site performance and site-to-site variability, interactive examination of potential factors associated with key observations and qualitative exploration of relationships among these factors. However, most visualization applications are aimed at computer-savvy experts and place a high technical burden on the typical end user. Broad-based adoption of visualization techniques by clinical teams requires: 1) intuitive interface with a quick learning curve; 2) rich functionality to support ad-hoc views and analyses; 3) pre-configured visualizations for common tasks; 4) rapid configuration and minimal delay in mapping data coming from investigational sites to enable timely review and intervention; 5) low technical resource demands and no increase in the workload of data management and clinical teams; 6) low licensing cost to enable widespread deployment under tight budgets; and 7) effective training and support by a knowledgeable and responsive team. In this talk, we describe Clinical Case, a new clinical trial monitoring application developed at Janssen R&D. Clinical Case was developed with the aforementioned design principles in mind, and represents a compelling solution to a significant unmet need.

TessellaNEW 10:05 A Day in the Life of a Data Scientist: Improving Translational InformaticsJamie MacPherson, Ph.D., Consultant, Tessella
Translational informatics integrates and interrogates multiple data assets across different stages in drug development; these assets are diverse in type, scale and quality.  To be efficient and effective, translational informatics projects must balance technical innovation and a practical ability to provide interpretable results. Here, we present a novel approach to translational informatics support: embedding 'Data Scientists' within drug-project teams.

10:20 Coffee Break

10:30 BioAssay Ontology (BAO)and the LINCS Information FramEwork (LIFE) to Integrate and Analyze Diverse High Throughput and Cellular Profiling Assay Data

Stephan Schürer, Ph.D., Center for Computational Science and Department of Molecular and Cellular Pharmacology, Miller School of Medicine, University of Miami

The lack of a established and accepted standards to describe and annotate biological assays and screening results in the domain ofhigh throughput and high content screening (HTS, HCS) is a severe limitation to utilize these valuable datasets to their maximum potential. We developed BioAssay Ontology (BAO:http://bioassayontology.org) to enable standardized description, integration and meta-analysis of various high throughput and profiling assay and screening results. BAO leverages Description Logic and Web Ontology Language to capture and formalize knowledge about assays and enable computational systems to utilize this knowledge. We illustrate our approach using data generated in the Library of Integrated Cellular Network-based Signatures (LINCS) Program, a recent large-scale systems biology data production and analysis effort funded by the NIH. Leveraging the ontology, we developed a semantic model to describe and integrate LINCS data. Weimplemented a semantic web software system, the LINCS Information FramEwork (LIFE: http://lifekb.org/) to exchange, query, and explore these datasets. Our approach facilitates the linking and classification of diverse entities, such small molecules, cellular model systems, diseases, gene and protein kinase targets, based on the underlying cellular profiling results.  

11:00 Secondary Research with Clinical Data

Shoibal Datta, Ph.D., Associate Director, R&D Information Technology, Biogen Idec

Biogen Idec has recently embarked on an ambitious strategy to embed translational approaches into every aspect of its R&D lifecycle. This has required a complete overhaul of processes and systems to support the strategy touching almost all functions within R&D. Key lessons and challenges as we progress will be presented.

11:30 OpenMedNet: Toward a Future of Personalized Medicine- Bridging Genomics, Informatics and Clinical Care

Andreas M. Kogelnik, M.D., Ph.D., Director, Open Medicine Institute

OpenMedNet is an integrated, HIPAA-compliant platform that allows researchers, healthcare providers and patients, to share information while enabling novel genomic research and rigorous clinical trials as well as supporting ongoing personalized clinical care. OpenMedNet aligns longitudinal data with a coordinated biobank.

12:00 pm Luncheon Presentations (Sponsorship Opportunities Available) or Lunch on Your Own


Data Integration 

1:15 Chairperson's Remarks

1:20 Synthetic Biology beyond the Firewall: Cloud-Based Computing with Extremely High Value Data

Michael Fero, Ph.D., CEO, TeselaGen Bio

This talk presents a use-case that illustrates the cost and time benefits of using 3rd party cloud based informatics solutions vs keeping high-value data behind corporate firewalls. Recommendations on how to implement secure solutions that ensure data integrity and security will also be presented.

1:50 Berg Interrogative Biology: Personalizing Healthcare by Using Advanced Molecular Analytics

Niven Narain, Ph.D., President and CTO, Berg Pharma

This talk will review implementation and case studies of a top-of-the-art unique analytical platform for healthcare and molecular informatics. Real world application of this Bayesian artificial intelligence based approach to data analysis of massive collections of patient records, clinical information and molecular measurements will be presented.

2:20 HOMER: A Free Software Suite Designed for Biologists to Analyze Next-Generation Sequencing Data of Epigenetics and Long-Range Genomic Interactions

Yin Lin, Ph.D., Assistant Project Scientist, Biological Sciences, University of California, San Diego

This talk will describe a proven free software suite to assist researchers in performing their own analyses on NGS data in a matter of hours for quality control, data visualization, generation of hypothesis, and to hasten the process of discovery.

3:20 Close of Conference

Day 1Day 2 | Day 3

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Premier Sponsors

Beckman Coulter Life Sciences 

Boston Healthcare



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Cofactor Genonics


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