The project is lead by Ned Talley (a program officer at NINDS) with support from Chalklabs, Indiana University, UC Irvine, U Mass and BIRN. For an overview of the methodology, see Database of NIH grants using machine-learned categories and graphical clustering, published in Nature Methods, May 2011.
To use this capability, go to www.nihmaps.org and click “Database”.
]]>For more information see healthgrid.org.
]]>The workshop will be led by the XNAT developers at Washington University along with several invited speakers and includes three separate tracks designed to interest both technical and non-technical attendees.
For more information, please go to:
]]>For more information see healthgrid.org.
]]>For more information about the workshop, see http://pipeline.loni.ucla.edu/training/cchmc2012/.
]]>You can view the paper here: http://www.nature.com/ng/journal/v44/n2/full/ng.1054.html
]]>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.
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:
]]>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.
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]]>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.
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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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]]>]]>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.
Title: REDCap at Emory University: Implementation of an enterprise service for study based electronic data capture
We invite you to attend a Web seminar from the CVRG, to be held on May 12, 2011. You are welcome to forward this on to all interested parties. More information on the webinar can be found on the CVRG website under CVRG Webinars.
Host: Stephen Granite
Date & Time: May 12, 2011 1:00 pm, Eastern Daylight Time (New York, GMT-04:00)
Event URL: Click here
Event number: 662 733 506
Event password: cvrg
Abstract:
The Research and Health Sciences IT Division (RHSIT) at Emory University supports multiple platforms and services to support research investigators across the university and the Atlanta Clinical and Translational Science Institute. RHSIT has deployed the Research Electronic Data Capture (REDCap) system as a hosted service and support data collection for a wide range of research studies. The division service includes initial consultation with investigators after which the investigator can choose to create and manage their own forms or utilize services provided by the division for form development. The division coordinates form-based data capture solutions with the investigator and the Biostatistics Department in the Emory Rollins School of Public Health to ensure data collection instruments meet overall study aims as well as data quality and downstream analysis requirements. RHSIT is also working on several initiatives to integrate form-based data capture with data from the Emory Healthcare Clinical Data Warehouse and a variety of clinical and research data sources.
In this seminar we will provide an overview of the Emory/RHSIT electronic data capture service and our utilization of REDCap as key tool in providing low cost services to investigators. We will also review our approach to research based data capture and management using a combination of technologies including REDCap.
Speaker Bios:
Tim Morris joined Emory University in February of 2008 as Director, Research Informatics in the Research and Health Sciences Information Technology Division after twenty years at the Centers for Disease Control and Prevention (CDC). He is currently leading several initiatives that support data capture and analysis for clinical research studies across the Emory University research community and is also the lead on an enterprise laboratory information system implementation. In his previous position at the CDC, Mr. Morris served as the director of the Division of Informatics Shared Services in the National Center for Public Health Informatics and directed the implementation of standards based enterprise systems for alerting and communication, terminology services and secure reliable messaging.
Kathryn Claypool joined Emory University Research and Health Sciences IT Division after 10 years in public health at both the state and federal levels. Her expertise with epidemiology, surveillance databases, and public health data collection provides a unique perspective when working with clinical researchers to plan and design their databases at Emory. She manages the enterprise REDCap implementation for Emory University and its affiliates and applies expertise gained through years of public health service to assist researchers at Emory to better design and execute their research databases to yield more structured and validated data for analysis.
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]]>We invite you to attend a Web seminar from the CVRG, to be held on April 14, 2011. 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: April 14, 2011 1:00 pm, Eastern Daylight Time (New York, GMT-04:00)
Event URL: Click here
Event number: 668 466 434
Abstract:
Service-oriented Science (SOS) represents a SOA approach to federating data access and analysis across different institutional and disciplinary sources, thus facilitating large scale scientific collaboration. The US National Cancer Institute?s Biomedical Information Grid (a.k.a., caBIG) program seeks to create both a service computing infrastructure (caGrid) and a suite of data and analytical services. Workflow tools in caGrid facilitate both the use and creation of services by accelerating service discovery, composition and orchestration tasks.
In this talk we use caGrid as a case of service computing in biomedical science and include a combination of research and engineering effort made by our team. The following aspects are to be covered: 1) the motivation of SOS and an overview of state-of-the-art; we will highlight some examples in biomedical and bioinformatics field; 2) caGrid architecture, the service creation and management tools it offers and the services it hosts; 3) Taverna workbench as the workflow solution of caGrid, and how we enhanced it to fulfill the requirements from caGrid community; 4) the challenges we faced and the lessons learned.
Speaker Bio:
Ravi Madduri is a Project Manager at the Mathematics and Computer Science Division of Argonne National Laboratory and a Fellow in the Computational Institute at the University of Chicago. Ravi is also a key player in the BIRN project and is the chair of the Workflow Working Group. He is actively involved in developing innovative software and networking technology. He developed a remote application virtualization infrastructure and is a key contributor to the Cancer Bioinformatics Grid (caBIG). The Grid-enable extension was incorporated in the Grid Service Authoring Toolkit (Introduce) and is used by NCI Information Systems.
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]]>BIRN Graphical Pipeline Workflow Capability for Computational Genomics and Visual Informatics
The BIRN Graphical Pipeline Workflow Capability for Computational Genomics and Visual Informatics capability allows BIRN users to design, execute, modify, and share openly advanced computational protocols for diverse types of informatics, imaging and genomics applications.
This page provides a self-contained and complete description that users should be able to follow if they want to reproduce any of the results, analyses or protocols distributed by colleagues as Pipeline Workflows (XML files). The supporting documents include a detailed documentation, a 1-page summary guide (both in PDF) as well as all pipeline workflows.
BIRN welcomes the community to review and provide any feedback on this.
]]>You can find the article here: http://www.frontiersin.org/neuroinformatics/10.3389/fninf.2010.00118/abstract
Below is the abstract:
]]>We describe an application of the BIRN mediator to the integration of neuroscience experimental data sources. The BIRN mediator is a general purpose solution to the problem of providing integrated, semantically-consistent access to biomedical data from multiple, distributed, heterogeneous data sources. The system follows the mediation approach, where the data remains at the sources, providers maintain control of the data, and the integration system retrieves data from the sources in real-time in response to client queries. Our aim with this paper is to illustrate how domain-specific data integration applications can be developed quickly and in a principled way by using our general mediation technology. We describe in detail the integration of two leading, but radically different, experimental neuroscience sources, namely, the human imaging database, a relational database, and the eXtensible neuroimaging archive toolkit, an XML web services system. We discuss the steps, sources of complexity, effort, and time required to build such applications, as well as outline directions of ongoing and future research on biomedical data integration.