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[ontolog-forum] NCBO Webinar: Rai Winslow, July 7, Ontology-Based Annota

To: "[ontolog-forum]" <ontolog-forum@xxxxxxxxxxxxxxxx>
From: Trish Whetzel <plwhetzel@xxxxxxxxx>
Date: Fri, 2 Jul 2010 17:20:11 -0700
Message-id: <AANLkTimjtqMOTAoUq3i0MRdblbQ4QE-nmlNMXlzWNI_8@xxxxxxxxxxxxxx>
The next NCBO Webinar will be held Wednesday, July 7 at 10:00am PT. Please note there will not be a VOIP option and attendees must call into the teleconference. The Webinar will be presented by Dr. Rai Winslow from Johns Hopkins University. The title of the presentation is "Ontology-Based Annotation of Biomedical Time-Series Data”. For a schedule of the 2010 presentations or for more information about the NCBO Seminar Series see: http://www.bioontology.org/seminar-series .  Below is information on how to join the online meeting via WebEx and accompanying teleconference.

An ECG is the time-varying electrical potential generated by the underlying electrical activity of the heart. It is one of the most common measurements made in cardiovascular clinical research.  ECG signals are usually measured by placing 3- or 12-lead electrodes on the torso and recording short time segments of electrical activity (~ 10 Sec). ECG signals may also be measured using a portable device known as a Holter monitor to obtain longer duration recordings (~ 24 hours).
Features of the ECG waveform provide important information on the electrical activity of the heart. The P-wave represents electrical activation of the atria. The QRS complex is generated as a wave of electrical activity propagates throughout the cardiac ventricles, producing mechanical contraction. The ST segment reflects the amount of time the ventricles remain electrically depolarized. The T-wave is generated as the myocardium recovers from electrical excitation. Changes in the properties of these ECG features are important indicators of abnormal heart activity. For example, prolongation of the QRS complex duration reflects slowed conduction in the heart. Prolongation of the QT interval is now known to be an important biomarker for risk of arrhythmia. Despite the diagnostic value of these data, there are no open, non-proprietary tools for its storage and dissemination. ECG data is collected and stored in a proprietary format using “heart stations”. Data stored in heart stations is difficult, and sometimes impossible, for users to access directly. Therefore, in most clinical studies, the only ECG data that is retained are values computed from the ECG time-series using analysis software integrated into the heart station (e.g., QT interval variability), images (jpegs, png’s, etc) of a few cycles of the ECG, or even paper recordings.
The CardioVascular Research Grid Project is developing tools for extracting ECG data from heart stations and storing it in digital form so that all the primary ECG time-series data collected in clinical research studies can be saved, analyzed using open-source software, and shared with others. In an NCBO Driving Biological Project, we are going beyond this work to develop an ontology for describing ECG data collection protocols, instrumentation, waveform features, and values calculated from the ECG signal. We are developing a web-interface, using the Google Web Toolkit (GWT), by which users can search for specific ECG data sets in data services, download these data from the services, visualize the data, select features of interest in the ECG waveform, annotate those features by accessing concepts in the ECG Ontology stored in BioPortal, and then store the annotated data back into data services. This infrastructure now makes it possible to save and disseminate carefully annotated primary digital ECG data sets. Annotation makes it possible for others to re-analyze the data in ways not intended in the original study. It also supports the integration of ECG primary and derived data across studies.
In this presentation, we will demonstrate these tools. We will describe: a) recent extensions to the ECG Ontology, including addition of new terms provided by the user community; b) integration of the Basic Formal Ontology; c) extensions to the web-interface made using the GWT; and d) application of these tools in what are now 9 large-scale NHLBI-funded clinical research projects.

Raimond Winslow is the Director of the Institute for Computational Medicine at Johns Hopkins University, and the Raj and Neera Singh Professor of Biomedical Engineering. He is PI of the CardioVascular Research Grid Project. His research interests are computational modeling of cardiac myocytes and tissue to understand the basis of arrhythmia and sudden cardiac death, and development of new approaches and tools for sharing data from cardiovascular clinical and basic research studies.
Stephen Granite is Project Manager of the CardioVascular Research Grid. His research interests are developing new technology supporting biomedical research grids, development of cardiovascular ontology, and portal engineering in life sciences applications.

Topic: NCBO Seminar Series
Date: July 7, 2010 
Time: 10:00 am, Pacific Daylight Time (San Francisco, GMT-07:00)
Meeting Number: 926 719 478
Meeting Password: ncbomeeting

To join the online meeting (Now from iPhones too!)
1. Go to https://stanford.webex.com/stanford/j.php?ED=107799137&UID=0&PW=NZDUwYTM4MmI3&RT=MiM0
2. Enter your name and email address.
3. Enter the meeting password: ncbomeeting
4. Click "Join Now".

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Global call-in numbers: https://stanford.webex.com/stanford/globalcallin.php?serviceType=MC&ED=107799137&tollFree=0

Access code:926 719 478

For assistance
1. Go to https://stanford.webex.com/stanford/mc
2. On the left navigation bar, click "Support".

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