Dec 5, Samir Courdy and Joyce Niland, Building NLP Processes for Auto Extraction of Data from Clinical Reports

BIOS:

Samir Courdy: Samir Courdy is the Chief Research Information Officer (CRIO), and Director of Research Informatics at the Huntsman Cancer Institute (HCI). Mr. Courdy joined the Institute in 1999.

Mr. Courdy is responsible for all aspects of software design and development for clinical, basic science, and population research at HCI. He coordinates the efforts of the Research Informatics Shared Resource to meet the needs and requirements of the Cancer Center, provides guidance and planning effort for each project, runs coordination meetings, manages staff, and provides strategic direction for architecture, projects, and technology.

Mr. Courdy has been at HCI for 15 years during which his team was responsible for the design and implementation of several systems, including an enhanced Research Subject Registry. A Biospecimen Tracking System (itBioPath), a translational research application for the Biorepository and Molecular Pathology Core BMP, and a Comprehensive Clinical Cancer Research System (CCR) with a robust and extensible meta-model enabling all cancer groups to co-exist in the same database, managed by a very complex security model which is compliant with IRB, and HIPPA regulations. The team released GNomEx a High Throughput Next Gen Sequencing LIMS system for use by the HCI and University of Utah community.

The team completed work on an analysis suite built upon the Integrated Genome Browser (IGB) and the Distributed Annotation System (DAS/2) along with an internally developed publishing suite GenoPub. GNomEx and GenoPub were both released as an open source project and are available for download on sourceforge. GNomEx was recently integrated with our BioSpecimen System (itBioPath) to provide linkages between genomic and clinical data. The development of a Chemical Screens Annotation and Management System (CSAM) was also completed within the last six months. Mr. Courdy is developing a natural language processing workflow for identifying and extracting clinical and diagnostic information from surgical pathology reports, physicians’ notes and radiology documents. This project is utilizing a third party software package from Linguamatics.

Prior to his service at HCI, he worked in the private sector in several roles including software engineering and development, in the areas of real time visual flight simulation for the US and foreign militaries, led teams responsible for developing large workflow software systems at Fidelity Investments. Part of the design and development team responsible for creating the Pathways Laboratory Information System at McKesson, known now as the Horizon Lab product line.

Joyce Niland: Dr. Joyce Niland is the first holder of the Edward & Estelle Alexander Endowed Chair in Information Sciences at City of Hope Comprehensive Cancer Center. She received her Bachelors degree in Human Biology from Stanford University, a Masters degree in Physical Therapy from University of Southern California (USC) and Masters and Doctoral degrees in Biometry from USC. She is an Associate Director of City of Hope Cancer Center, Full Professor in the Beckman Research Institute, and adjunct Professor in the USC Keck School of Medicine. Dr. Niland chairs the Department of Information Sciences, including the Divisions of Biostatistics, Clinical Research Information Management, and Research Informatics and Systems. In 2013 she was promoted to Chief Research Information Officer for City of Hope.

Dr. Niland has over 30 years of experience collaborating in translational research. She has published more than 140 biomedical research papers, numerous book chapters, and a text on informatics tools for clinical trials. She directed the National Comprehensive Cancer Center Network Outcomes Research Data Coordinating Center (DCC) for 15 years, and currently directs national DCCs for the Integrated Islet Distribution Program for Type 1 diabetes research, the Intestinal Stem Cell research consortium, and the Human Islet Research Network. Dr. Niland is on advisory boards for the Clinical Data Interchange Standards Consortium (CDISC), the Computational Statistics and Data Analysis (CSDA) journal, and the American Society of Clinical Oncology (ASCO) CancerLinq system. She is an elected Fellow of the American Statistical Association (ASA) and has served as Vice President of ASA and Scientific Secretary of the International Association of Statistical Computing. In 2004 she received the City of Hope Medical and Scientific Achievement award for her contributions to biomedical research.

SUMMARY:

Topic: A Systematic Approach to Building Natural Language Processing (NLP) Processes for Automated Extraction of Data from Clinical Reports

Speakers: Samir Courdy, Chief Research Information Officer and Director of Research Informatics, Huntsman Cancer Institute, and Joyce Niland, Ph.D., Researcher, City of Hope

Date: Wednesday, December 5, 2018

Time: 11:00 a.m. – 12:00 p.m. ET

Room: 1W032-034

WebEx: https://cbiit.webex.com/cbiit/onstage/g.php?MTID=e00956dd57152576cc40d71c1ebc4fdbc

Event ID: 733 960 637

Event Password: $Peakerseries18

You are invited to listen to Dr. Niland and Mr. Courdy's presentation in the NCI Shady Grove Building on Medical Center Drive or via WebEx. Dr. Niland and Mr. Courdy will present remotely via WebEx.

Presentation: A screencast of the presentation will be available for viewing after the event on the NCI CBIIT Speaker Series YouTube Playlist.

About the NCI CBIIT Speaker Series:

The National Cancer Institute (NCI) Center for Biomedical Informatics and Information Technology (CBIIT) Speaker Series presents talks from innovators in the research and informatics communities. The biweekly presentations allow thought leaders to share their work and discuss trends across a diverse set of domains and interests. The goals of the Speaker Series are: to share leading-edge research; to inform the community of new tools, trends, and ideas; to inspire innovation, and to provide a forum from which new collaborations can begin. For additional information, including past speaker series presentations, visit the CBIIT Speaker Series page.

Individuals with disabilities who need reasonable accommodation to participate in this program should contact the Office of Space and Facilities Management (OSFM) at 240-276-5900 or the Federal TTY Relay number 1-800-877-8339.

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