skip to main content
OSTI.GOV title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: ORBiT: Oak Ridge biosurveillance toolkit for public health dynamics

Journal Article · · BMC Bioinformatics
 [1];  [1];  [2];  [2];  [3];  [3];  [4]
  1. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Computational Science and Engineering Division; Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Health data Sciences Inst.
  2. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Computational Science and Engineering Division
  3. Univ. of Pittsburgh, PA (United States). Dept. of Computational & Systems Biology
  4. IMS Government Solutions, Plymouth Meeting, PA (United States)
+ Show Author Affiliations

Background: The digitization of health-related information through electronic health records (EHR) and electronic healthcare reimbursement claims and the continued growth of self-reported health information through social media provides both tremendous opportunities and challenges in developing effective biosurveillance tools. With novel emerging infectious diseases being reported across different parts of the world, there is a need to build systems that can track, monitor and report such events in a timely manner. Further, it is also important to identify susceptible geographic regions and populations where emerging diseases may have a significant impact. Methods: In this paper, we present an overview of Oak Ridge Biosurveillance Toolkit (ORBiT), which we have developed specifically to address data analytic challenges in the realm of public health surveillance. In particular, ORBiT provides an extensible environment to pull together diverse, large-scale datasets and analyze them to identify spatial and temporal patterns for various biosurveillance-related tasks. Results: We demonstrate the utility of ORBiT in automatically extracting a small number of spatial and temporal patterns during the 2009-2010 pandemic H1N1 flu season using claims data. These patterns provide quantitative insights into the dynamics of how the pandemic flu spread across different parts of the country. We discovered that the claims data exhibits multi-scale patterns from which we could identify a small number of states in the United States (US) that act as “bridge regions” contributing to one or more specific influenza spread patterns. Similar to previous studies, the patterns show that the south-eastern regions of the US were widely affected by the H1N1 flu pandemic. Several of these south-eastern states act as bridge regions, which connect the north-east and central US in terms of flu occurrences. Conclusions: These quantitative insights show how the claims data combined with novel analytical techniques can provide important information to decision makers when an epidemic spreads throughout the country. Taken together ORBiT provides a scalable and extensible platform for public health surveillance.

Research Organization:
Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)
Sponsoring Organization:
USDOE Office of Science (SC), Advanced Scientific Computing Research (ASCR)
Grant/Contract Number:
AC05-00OR22725
OSTI ID:
1626302
Journal Information:
BMC Bioinformatics, Vol. 16, Issue S17; ISSN 1471-2105
Publisher:
BioMed CentralCopyright Statement
Country of Publication:
United States
Language:
English

References (32)

Subsystem Identification Through Dimensionality Reduction of Large-Scale Gene Expression Data journal July 2003
Wikipedia Usage Estimates Prevalence of Influenza-Like Illness in the United States in Near Real-Time journal April 2014
Social and News Media Enable Estimation of Epidemiological Patterns Early in the 2010 Haitian Cholera Outbreak journal January 2012
BioCaster: detecting public health rumors with a Web-based text mining system journal October 2008
Using Web Search Query Data to Monitor Dengue Epidemics: A New Model for Neglected Tropical Disease Surveillance journal May 2011
Crowdsourcing, citizen sensing and sensor web technologies for public and environmental health surveillance and crisis management: trends, OGC standards and application examples journal January 2011
Potential for the International Spread of Middle East Respiratory Syndrome in Association with Mass Gatherings in Saudi Arabia journal January 2013
The 2014 Ebola virus disease outbreak in West Africa journal August 2014
ProMED-mail: An Early Warning System for Emerging Diseases journal July 2004
Security and Privacy Issues with Health Care Information Technology
  • Meingast, Marci; Roosta, Tanya; Sastry, Shankar
  • Conference Proceedings. Annual International Conference of the IEEE Engineering in Medicine and Biology Society, 2006 International Conference of the IEEE Engineering in Medicine and Biology Society https://doi.org/10.1109/iembs.2006.260060
conference August 2006
Reassessing Google Flu Trends Data for Detection of Seasonal and Pandemic Influenza: A Comparative Epidemiological Study at Three Geographic Scales journal October 2013
Outpatient influenza antiviral prescription trends with influenza-like illness in the USA, 2008–2010 journal March 2014
Privacy, Confidentiality, and Electronic Medical Records journal March 1996
Twitter as a Sentinel in Emergency Situations: Lessons from the Boston Marathon Explosions journal January 2013
The Use of Twitter to Track Levels of Disease Activity and Public Concern in the U.S. during the Influenza A H1N1 Pandemic journal May 2011
Integrating Phylodynamics and Epidemiology to Estimate Transmission Diversity in Viral Epidemics journal January 2013
Statistical Challenges Facing Early Outbreak Detection in Biosurveillance journal February 2010
The Parable of Google Flu: Traps in Big Data Analysis journal March 2014
Surveillance for Influenza during the 2009 Influenza A (H1N1) Pandemic-United States, April 2009-March 2010 journal December 2010
Making the most of a brave new world: Opportunities and considerations for using Twitter as a public health monitoring tool journal June 2014
Innovative Uses of Electronic Health Records and Social Media for Public Health Surveillance journal February 2014
Comparison: Flu Prescription Sales Data from a Retail Pharmacy in the US with Google Flu Trends and US ILINet (CDC) Data as Flu Activity Indicator journal August 2012
Spatial Transmission of 2009 Pandemic Influenza in the US journal June 2014
The Effectiveness of U.S. Public Health Surveillance Systems for Situational Awareness during the 2009 H1N1 Pandemic: A Retrospective Analysis journal August 2012
Inferring the Source of Transmission with Phylogenetic Data journal December 2013
Detecting influenza epidemics using search engine query data journal February 2009
Harnessing Electronic Health Records for Public Health Surveillance journal December 2011
A New Approach to Monitoring Dengue Activity journal May 2011
The AFHSC-Division of GEIS Operations Predictive Surveillance Program: a multidisciplinary approach for the early detection and response to disease outbreaks journal January 2011
Identification and investigation of disease outbreaks by ESSENCE journal March 2003
HealthMap: Global Infectious Disease Monitoring through Automated Classification and Visualization of Internet Media Reports journal March 2008
Aligning temporal data by sentinel events conference April 2008

Cited By (3)

Data-driven efficient network and surveillance-based immunization journal January 2019
A systematic review of spatial decision support systems in public health informatics supporting the identification of high risk areas for zoonotic disease outbreaks journal October 2018
Discovering Multi-Scale Co-Occurrence Patterns of Asthma and Influenza with Oak Ridge Bio-Surveillance Toolkit journal August 2015

Similar Records

Related Subjects

97 MATHEMATICS AND COMPUTING
Biochemistry & Molecular Biology
Biotechnology & Applied Microbiology
Mathematical & Computational Biology