Chunju Tseng

West Nile Virus and Botulism Portal: A Case Study in Infectious Disease Informatics

Information technologies and infectious disease informatics are playing an increasingly important role in preventing, detecting, and managing infectious disease outbreaks. This paper presents a collaborative infectious disease informatics project called the WNV-BOT Portal system. This Portal system provides integrated, Web-enabled access to a variety of distributed data sources related to West Nile Virus and Botulism. It also makes available a preliminary set of data analysis and visualization tools tailored for these two diseases. This system has helped to demonstrate the technological feasibility of developing a cross jurisdiction and cross species infectious disease information infrastructure and identify related technical and policy-related challenges with its national implementation.

System for Infectious Disease Information Sharing and Analysis: Design and Evaluation

Motivated by the importance of infectious disease informatics (IDI) and the challenges to IDI system development and data sharing, we design and implement BioPortal, a Web-based IDI system that integrates cross-jurisdictional data to support information sharing, analysis, and visualization in public health. In this paper, we discuss general challenges in IDI, describe BioPortals architecture and functionalities, and highlight encouraging evaluation results obtained from a controlled experiment that focused on analysis accuracy, task performance efficiency, user information satisfaction, system usability, usefulness, and ease of use.

Incorporating geographical contacts into social network analysis for contact tracing in epidemiology: a study on Taiwan SARS data

In epidemiology, contact tracing is a process to control the spread of an infectious disease and identify individuals who were previously exposed to patients with the disease. After the emergence of AIDS, Social Network Analysis (SNA) was demonstrated to be a good supplementary tool for contact tracing. Traditionally, social networks for disease investigations are constructed only with personal contacts. However, for diseases which transmit not only through personal contacts, incorporating geographical contacts into SNA has been demonstrated to reveal potential contacts among patients. In this research, we use Taiwan SARS data to investigate the differences in connectivity between personal and geographical contacts in the construction of social networks for these diseases. According to our results, geographical contacts, which increase the average degree of nodes from 0 to 108.62 and decrease the number of components from 961 to 82, provide much higher connectivity than personal contacts. Therefore, including geographical contacts is important to understand the underlying context of the transmission of these diseases. We further explore the differences in network topology between one-mode networks with only patients and multi-mode networks with patients and geographical locations for disease investigation. We find that including geographical locations as nodes in a social network provides a good way to see the role that those locations play in the disease transmission and reveal potential bridges among those geographical locations and households.

Visualization in law enforcement

Visualization techniques have proven to be critical in helping crime analysis. By interviewing and observing Criminal Intelligence Officers (CIO) and civilian crime analysts at the Tucson Police Department (TPD), we found that two types of tasks are important for crime analysis: crime pattern recognition and criminal association discovery. We developed two separate systems that provide automatic visual assistance on these tasks. To help identify crime patterns, a Spatial Temporal Visualization (STV) system was designed to integrate a synchronized view of three types of visualization techniques: a GIS view, a timeline view and a periodic pattern view. The Criminal Activities Network (CAN) system extracts, visualizes and analyzes criminal relationships using spring-embedded and blockmodeling algorithms. This paper discusses the design and functionality of these two systems and the lessons learned from the development process and interaction with law enforcement officers.

SpidersRUs: automated development of vertical search engines in different domains and languages

In this paper we discuss the architecture of a tool designed to help users develop vertical search engines in different domains and different languages. The design of the tool is presented and an evaluation study was conducted, showing that the system is easier to use than other existing tools

SpidersRUs: Creating specialized search engines in multiple languages

While small-scale search engines in specific domains and languages are increasingly used by Web users, most existing search engine development tools do not support the development of search engines in languages other than English, cannot be integrated with other applications, or rely on proprietary software. A tool that supports search engine creation in multiple languages is thus highly desired. To study the research issues involved, we review related literature and suggest the criteria for an ideal search tool. We present the design of a toolkit, called SpidersRUs, developed for multilingual search engine creation. The design and implementation of the tool, consisting of a Spider module, an Indexer module, an Index Structure, a Search module, and a Graphical User Interface module, are discussed in detail. A sample user session and a case study on using the tool to develop a medical search engine in Chinese are also presented. The technical issues involved and the lessons learned in the project are then discussed. This study demonstrates that the proposed architecture is feasible in developing search engines easily in different languages such as Chinese, Spanish, Japanese, and Arabic.

The BioPortal project: a national center of excellence for infectious disease informatics

In this project summary, we briefly present the technical objectives and accomplishments of our Infectious Disease Informatics project. We describe the inter-agency, inter-disciplinary, and academia-government partnerships critical to project success and discuss the broader application context for this research.

BioPortal: a case study in infectious disease informatics

We present the BioPortal system, an integrated cross-jurisdictional data sharing and analysis environment to facilitate detection, prevention, and management of infectious disease outbreaks

A web-based system for infectious disease data integration and sharing: evaluating outcome, task performance efficiency, user information satisfaction, and usability

To better support the surveillance of infectious disease and epidemic outbreaks by public health professionals, we design and implement BioPortal, an advanced Web-based system for cross-jurisdictional information sharing and integration. In this paper, we report two empirical studies that evaluate the outcomes, task performance efficiency, user information satisfaction, and usability associated with BioPortal. Overall, our results suggest that the use of BioPortal can improve users’ surveillance performance as measured by analysis accuracy and efficiency (i.e., the amount of time required to complete an analysis task). Our subjects were highly satisfied with the information support of BioPortal and considered it reasonably usable. Our evaluation findings show the effectiveness and value of BioPortal and, at the same time, shed light on several areas where its design can further improve.

Global foot-and-mouth disease surveillance using bioportal

The paper presents a description of the FMD BioPortal biosurveillance system (http://fmd.ucdavis.edu/bioportal/) that is currently operating to capture, analyze, and disseminate global data on foot-and-mouth (FMD) disease. The FMD BioPortal makes available to users world-wide FMD-related data from the Institute for Animal Health at Pirbright, England. The systems tools include those for tabulating and graphing data, performing spatio-temporal cluster analysis of outbreak cases of FMD, and analyzing genomic changes in FMD viruses. The FMD BioPortal also includes the FMD News (http://fmd.ucdavis. edu/index.php?id=1), which is a near real time web search to identify and capture FMD-related news items appearing worldwide. Major systems components include a communication backbone for secure, real-time data transfer, a data analysis module that can run analytical programs to assess spatial-temporal clustering, and an interactive visualization tool for integrated analysis and display of epidemiological and genomic data.