You can view the paper here: http://www.biomedcentral.com/1471-2105/12/304

http://www.frontiersin.org/neuroinformatics/10.3389/fninf.2011.00024/abstract

Below is the abstract:

This paper describes software for neuroanatomical knowledge synthesis based on neural connectivity data. This software supports a mature methodology developed since the early 1990s. Over this time, the Swanson laboratory at USC has generated an account of the neural connectivity of the sub-structures of the hypothalamus, amygdala, septum, hippocampus, and bed nucleus of the stria terminalis. This is based on neuroanatomical data maps drawn into a standard brain atlas by experts. In earlier work, we presented an application for visualizing and comparing anatomical macro connections using the Swanson third edition atlas as a framework for accurate registration. Here we describe major improvements to the NeuARt application based on the incorporation of a knowledge representation of experimental design. We also present improvements in the interface and features of the data mapping components within a unified web-application. As a step toward developing an accurate sub-regional account of neural connectivity, we provide navigational access between the data maps and a semantic representation of area-to-area connections that they support. We do so based on an approach called “Knowledge Engineering from Experimental Design” (KEfED) model that is based on experimental variables. We have extended the underlying KEfED representation of tract-tracing experiments by incorporating the definition of a neuronanatomical data map as a measurement variable in the study design. This paper describes the software design of a web-application that allows anatomical data sets to be described within a standard experimental context and thus indexed by non-spatial experimental design features.

https://wiki.birncommunity.org/x/SgNrAQ

http://www.birncommunity.org/about/birn-video-intro/

HID-Genetics: A Federated BIRN-enabled Data Management System for Clinical, Imaging, and Genome-Wide Association Studies
Keator D.B., Chen J., Ashish N., Torri F., Lakatos A., Potkin S.G., Macciardi F., Wei D.
(P087, PDF)

Do ontological concepts stand up to a meta-analysis of neuroimaging data?
Jessica A. Turner, Peter T. Fox, Christian F. Beckmann, Stephen M. Smith, Angela R. Laird
(P115, PDF)

BioScholar: a user-centered biocuration and knowledge management system that uses models of experimental design to drive knowledge acquisition and literature mining
Marcelo Tallis, Cartic Ramakrishnan, Thomas Russ, and Gully Burns
(Poster number TBD, PDF)

Knowledge Engineering Tools for Reasoning with Scientific Observations and Interpretations: a Neural Connectivity Use Case.

Written by Thomas A Russ, Cartic Ramakrishnan, Eduard H Hovy, Mihail Bota and Gully APC Burns for the Biomedical Informatics Research Network.

Published in BMC Bioinformatics 2011, 12:351doi:10.1186/1471-2105-12-351. 2011 Aug 22

You can read the abstract here:

http://www.biomedcentral.com/1471-2105/12/351

Title: Creating Semantically-enabled Registry Databases from EHR systems for Clinical and Translational Research.

We invite you to attend a Web seminar from the CVRG, to be held on August 11, 2011 at 1:00pm EDT.  You are welcome to forward this e-mail on to all interested parties. More information on the webinar can be found on the CVRG homepage, under CVRG Webinars.

Host: Stephen Granite
Date & Time: August 11, 2011 1:00 pm Eastern Daylight Time (New York, GMT-04:00)
Event URL: Click here
Event number: 660 710 961
Event password: cvrg

Abstract:

In the CTSA era there is great interest in aggregating and comparing populations across institutions. These sites likely represent data differently in their clinical data warehouses and other databases. Clinical data warehouses frequently are structured in a generalized way that supports many constituencies. For research, there is a need to transform these heterogeneous data into a shared representation, and to perform categorization and interpretation to optimize the data representation for investigators. We are addressing this need by extending an existing clinical database query system, PROTEMPA, that can execute temporal queries and extract longitudinal summaries of patient data. The extended system allows specifying data types of interest in federated databases, extracting the data into a shared representation, transforming it through categorization and interpretation, and loading it into a registry database that can be refreshed. Such a registry’s access control, data representation and query tools can be tailored to the needs of research while keeping local databases as the source of truth.

Speaker Bio:

Andrew Post is an MD- and PhD-trained researcher in Biomedical Informatics. His research focuses on clinical data warehouses and querying of temporal patterns in time-stamped patient data. He is Chief Clinical/Translational Informatics Architect of the Emory Center for Comprehensive Informatics and works closely with Emory Healthcare in providing clinical informatics expertise in quality improvement projects. He is faculty lead of the Analytic Information Warehouse at Emory Healthcare, and he leads the Enhanced Registries effort of the Atlanta Clinical and Translational Science Institute.

To join the online event:

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2. Click "Join Now".

For assistance

You can contact Stephen Granite at:
sgranite@jhu.edu

The playback of UCF (Universal Communications Format) rich media files requires appropriate players. To view this type of rich media files in the meeting, please check whether you have the players installed on your computer by going to https://icm.webex.com/icm/onstage/systemdiagnosis.php

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IMPORTANT NOTICE: This WebEx service includes a feature that allows audio and any documents and other materials exchanged or viewed during the session to be recorded. By joining this session, you automatically consent to such recordings. If you do not consent to the recording, discuss your concerns with the meeting host prior to the start of the recording or do not join the session. Please note that any such recordings may be subject to discovery in the event of litigation.

Title: Atrial Fibrillation: An Old Disease with New Challenges

We invite you to attend a Web seminar from the CVRG, to be held on July 14, 2011 at 1pm EDT. You are welcome to forward this e-mail on to all interested parties. More information on the webinar can be found on the CVRG homepage, under CVRG Webinars.

Host: Stephen Granite
Date & Time: July 14, 2011 1:00 pm Eastern Daylight Time (New York, GMT-04:00)
Event URL: Click here
Event number: 666 942 314
Event password: cvrg

Abstract:

Atrial fibrillation, a very common cardiac arrhythmia, has recently emerged as a new epicenter of clinical, engineering, and basic science research. This emergence is fueled by new results from experiments, animal models of the disease, and multimodal measurements in patients, catalyzed by rapid developments in interventional approaches to treatment. Our understanding of the disease is growing but still inadequate to provide satisfactory patient care and so there is enormous opportunity for a range of research approaches. Some attributes of the disease also make it a simultaneously compelling, accessible, and challenging target for inquiry; atrial fibrillation emerges only as a result of long term changes in tissue substrate, is triggered by remote ectopic activity, involves one or more mechanisms of cardiac arrhythmias, has a variable time course in individuals, and is both damaging to immediate quality of life and a major risk for secondary disease. The goal of this presentation will be to provide an overview of the disease and its putative mechanisms, to outline the range of inquiry possible and necessary, and then to emphasize the image based approaches that characterize the CARMA approach to understanding and treating atrial fibrillation. The intended audience includes any students or researchers with a basic understanding of cardiac function and electrophysiology with interest in this disease.

Speaker Bio:

Rob MacLeod was trained in physics, electrical engineering, and physiology & biophysics and is an associate professor of Bioengineering and Internal Medicine (Cardiology) at the University of Utah. He is an associate director of the Scientific Computing and Imaging (SCI) Institute and the Nora Eccles Harrison Cardiovascular Research and Training Institute (CVRTI). He is also an associate chairman and director of the undergraduate program in Biomedical Engineering and recently co-founded the Center for Arrhythmia Research and Management (CARMA). His research interests include computational electrocardiography (forward and inverse problems), experimental investigation and clinical detection of cardiac ischemia, repolarization abnormalities, cardiac arrhythmias, both atrial and ventricular, and defibrillation. For his research, he uses a broad range of techniques including scientific computing, imaging, image and signal processing, and visualization and well as experimental approaches in cardiac electrophysiology.

To join the online event:

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2. Click "Join Now".

For assistance

You can contact Stephen Granite at:
sgranite@jhu.edu

The playback of UCF (Universal Communications Format) rich media files requires appropriate players. To view this type of rich media files in the meeting, please check whether you have the players installed on your computer by going to https://icm.webex.com/icm/onstage/systemdiagnosis.php

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IMPORTANT NOTICE: This WebEx service includes a feature that allows audio and any documents and other materials exchanged or viewed during the session to be recorded. By joining this session, you automatically consent to such recordings. If you do not consent to the recording, discuss your concerns with the meeting host prior to the start of the recording or do not join the session. Please note that any such recordings may be subject to discovery in the event of litigation.

Helmer KG, Ambite JL, Ames J, Ananthakrishnan R, Burns G, Chervenak AL, Foster I, Liming L, Keator D, Macciardi F, Madduri R, Navarro JP, Potkin S, Rosen B, Ruffins S, Schuler R, Turner JA, Toga A, Williams C, Kesselman C. for the Biomedical Informatics Research Network. (2011) Enabling collaborative research using the Biomedical Informatics Research Network (BIRN). J Am Med Inform Assoc. 2011 Apr 22; [Epub ahead of print] PMID: 21515543.