Informatics Laboratory Research Articles

Automating Indicator Data Reporting from an EMR to Aggregate Data System Using OpenMRS and DHIS2

Background and Purpose: Electronic HIS are considered essential for managing health information. However, due to challenges of implementing interoperability across HIS, often electronic data are manually printed and re-entered into aggregate data systems. In 2009, World Health Organization (WHO) developed Statistical Data and Metadata Exchange for Health Domain (SDMX-HD) to facilitate health indicator exchange. To date, no documented implementation has demonstrated a practical application of SDMX-HD in automating indicator data reporting. This study demonstrates the use of OpenMRS, to generate and transmit indicator data to DHIS2 using key principles of SDMX-HD. Methods : We deployed OpenMRS and DHIS2 in a test environment at the US Centers for Disease Control and Prevention (CDC) Public Health Informatics Laboratory. OpenMRS was configured to send aggregate indicator data using DHIS reporting module and DHIS2 was prepared to receive them. The two applications were then linked and data exchange process was initiated in OpenMRS using demo data. Results : Fourteen data elements with disaggregation were generated and transmitted to DHIS2 successfully. A report with the 14 data elements was accurately generated from DHIS2. Discussions : Results indicate that indicator data can be sent automatically from OpenMRS to DHIS2, eliminating manual data entry. The success of this test will help evaluate the impact of implementing an automated generation of reporting indicators to reduce human resources needed to fulfill reporting requirements; and to improve data quality, completeness and timeliness. These impacts demonstrate that HIS scale-up can have a positive role in improving health service delivery, M&E, and public health planning. Keywords: Health information systems, Electronic medical records, Data exchange, Indicators, Resource-constrained settings, Aggregate data

‘Rew’ (Immémorial #6): what is surfacing and submerging

Immémorial is a work in progress which was begun in 1996, written, conceived and created by Pascale Weber and which deals with memory and identity. Its six versions question the interactions between technology, science and creation. 'Rew' is the title of the sixth version. As an abbreviation of 'Rewind', it raises the spectre of travelling back in the past, of accessing our childhood secrets, of revisiting, maybe rewriting our identity. Immémorial #6: 'Rew' was shown in Marseille (Friche de la Belle de Mai) during the 2012 Music Festival, following a two-year residency at the Experimental Music Group of Marseille [GMEM], Euphonia and the Music and Informatics Laboratory of Marseille [MIM]. The background and the lastest version of Immémorial allow us to investigate the relationship between technology, science and humanities. Science and the computer offer an emotional, aesthetical energy, a capacity to nourish poetry and imagination; the artist may intuitively propose free hypotheses, confronting his artistic project with scientific questioning, instead of giving meaning to his work. Doing so, he collaborates in the development of knowledge. Immémorial proposes a taxonomy of models of recollections which form our identity and deals with the dynamic functioning of our memory. Conversely, the structure of the computer language used for distributing the video image and sound spatialization guide the construction of the narrative and the return of the memorial experience in the device. Owing to the technical process of audio and visual spatialization, Immémorial projects the viewer into the heart of an environment, which is divided into 24 memorial moods based on poignant experiences, in order to awaken long-term memory. Immersive experiences pull us out of a reality too complex to grasp. This is the world narrowed in the heart of an enclosed space, a metaphor for a major societal issue: can we finally see the world as a plurality? Can we think outside of one’s body, from other bodies, from a common body?

Evidências de validade da Bateria Informatizada de Linguagem Oral com prova de raciocínio

Este estudo buscou relacionar a compreensão da linguagem oral com a habilidade de raciocinar, visando evidenciar validade correlacional para a Bateria Informatizada de Linguagem Oral por meio da associação com a Escala de Maturidade Mental Colúmbia. Participaram do estudo 82 alunos com idade entre 5 e 9 anos (M=7,05; DP=1,25), sendo 47,6% do sexo feminino. Frequentavam o pré (31,7%) e a 1ª (32,9%) e 2ª (35,4%) séries do Ensino Fundamental de escola pública do interior paulista. Aplicou-se coletivamente a Bateria e individualmente a Escala de Maturidade Mental Colúmbia. A Análise de Variância, por série, indicou diferença significativa para as provas de Compreensão Morfossintática, Sequência Lógica, Organização Lógico-Verbal e escore total da Bateria. A análise de regressão revelou que o raciocínio geral representa 29% das habilidades necessárias para um bom desempenho na Bateria. Verificou-se correlação baixa entre escores totais da Bateria e do Colúmbia, porém muito significativa. Constataram-se evidências de validade correlacional e de critério, para a Bateria.

The Application of a Telemedicine Management System: The Case of a Moroccan Hospital Unit

ABSTRACT This study is a contribution to the ongoing debate on the application of informatics in medicine. It attempts to outline a theoretical framework supported by a software application of a telemedicine management system. The proposed model is based on a detailed benchmarking of Telecom environments, hardware environments, and content management systems. This approach, which uses open source technologies, helps to create an interface with two entities: web and medical care USB. In sum, for the proposed telemedicine model to be successful, health professionals, telecom operators and research medical informatics laboratories must play an active role in the conception and implementation of telemedicine applications.

The 2012 Wisconsin Gubernatorial Recall Twitter Corpus

In the following document we detail what we identify as the Wisconsin Gubernatorial Recall Twitter Corpus. This dataset represents two and half months of collection surrounding and incorporating the June 2012 Wisconsin Gubernatorial Election collected using the Group Informatics Lab Infrastructure TwitterZombie at Drexel University (Black, Mascaro, Gallagher, & Goggins, 2012). This document is a precis for the larger dataset. We intend this document to be a way share with other researchers the type of syntactical feature use we identified in a statewide political race that many deemed to have national implications in a General Election year. Through this sharing we hope to build on existing knowledge about political discourse on Twitter and we welcome any researchers who are interested in collaborating in this space.

The ‘ripple effect’ of introducing evidence-based medicine into a curriculum

Context and setting The practice of medicine in Pakistan is guided by expert opinion, giving rise to an environment defined by the dictum ‘the professor is always right’. Evidence-based medicine (EBM) has not been recognised as a competency in most Pakistani medical school curricula. As we have the benefit of being imbedded in an innovative institution, we designed an educational experience in EBM with the aim of encouraging students to use scientific inquiry to question common clinical practices. Why the idea was necessary The college mission clearly states its goal of graduating students who are ready to practise medicine in the 21st century. Although the importance of evidence-based practice has been well documented in the literature, formal teaching of EBM in our curricula was non-existent. What was done The strategy included a plan for educating both faculty and students. Four internal medicine faculty members, trained in EBM, conducted a small-group workshop for 12 interested clinical faculty staff. Subsequently, two of the original trainers provided two ‘EBM for Beginners’ workshops for 21 students each, prior to the students’ fifth (final) year clinical clerkships. Students learned to ‘ask a well-built, searchable clinical question’ and ‘acquire the appropriate evidence’ on MEDLINE using various search strategies – the first two steps of the four EBM practice model steps. The workshops were conducted in an informatics laboratory equipped with 20 online work stations. A student handbook was developed for quick reference. Evaluation of results and impact Gains in faculty’s knowledge of and skills in EBM were assessed by pre- and post-workshop Berlin questionnaires. During the EBM for Beginners workshops, students completed a questionnaire that assessed their baseline computer skills, knowledge about study designs, and perceptions about the use of evidence in patient care. Students also completed a pre- and post-workshop paper case that required them to search MEDLINE in order to answer items pertaining to developing a clinical question and acquiring appropriate evidence. At the end of the workshop, self-rated skills and attitudes were also recorded on a retrospective pre- and post-test. Five months post-workshop, students self-rated their EBM skills and attitudes. In the first year of implementation, we demonstrated that both faculty and students could learn relatively quickly to apply the first two steps of EBM. The workshops were welcomed by both students and faculty. After the workshop, students expressed concerns that doctors in Pakistan may not be familiar with the idea of EBM. In addition to these intended outcomes, there were several other ways that this educational intervention affected behaviour within and the environment of our institution. The workshops brought the word ‘evidence’ to the fore in an environment not generally conducive to the questioning of clinical practices. Informal observation of routine clinical teaching indicated that faculty and students began to request evidence for clinical practices in clinical teaching activities. The effect rippled on to the College of Nursing’s research module, internal medicine morning reports, generating interest in medical education projects and international recognition of the institution at medical education conferences at which several oral and poster presentations were made. The project was eventually incorporated into the newly implemented integrated medical curriculum.

Outlook on Thailand's Genomics and Computational Biology Research and Development

With a wealth of biodiversity, a long tradition of agriculture-based industries, and an established medical and biotechnological research and development community, Thailand has become an attractive location for life sciences investment. The large amount of data generated in many areas of life sciences requires visualization, management, and analysis, principally through bioinformatics. To become successful, Thailand's research community should emphasize establishing core technologies, such as genomics and bioinformatics, to boost development of agriculture, food processing, and biomedical research. The Thai government realized the importance of this field and created a national policy to greatly increase Thailand's participation in bioinformatics and genomics, budgeting for specific development goals in research infrastructure, education, and sustainable human resources. Thailand has not lagged behind in bioinformatics research activity and recognizes the importance of bioinformatics through increased policy awareness, human resources development, and increased research activity involving genomic-scale data generation and computational analyses. Many applications of genomics and bioinformatics to biomedical research and development in Thailand have progressed substantially during the past few years, leading to successful applications in some specific local areas. However, the applications to other important areas, such as agriculture, are hampered by the limited availability of genomic sequence data and the lack of necessary biochemical/physiological information. With the advent of more and more genomic information in public databases, Thailand's research community is striving to adopt comparative genomics to obtain information of direct relevance to the country's health and industrial needs. This article highlights Thailand's contribution to genomics and bioinformatics in the following areas: (1) policy support from the Thai government, (2) capacity building through infrastructure/education/human resources, and (3) research and development in genomics and computational biology. (See Box 1 for Authors' Biographies). Box 1. Authors' Biographies Wannipha Tongsima, M.S., obtained her master's degree in Industrial Microbiology from Chulalongkorn University, Thailand. She was involved in founding the Bioinformatics research program in BIOTEC. To reinforce the research activity in this area, she also helped organize the first International Conference on Computational Biology (InCoB), held in Bangkok in 2002. Later, she was appointed to manage one of the first BIOTEC ethnic-specific human genetic variation programs, named the Thailand SNP Discovery Project. She works as a Genomic Medicine program coordinator for the Cluster and Program Management Office (CPMO) of the National Science and Technology Development Agency (NSTDA), which is an umbrella organization of four other national research centers in Thailand, including BIOTEC. Sissades Tongsima, Ph.D., received his doctoral degree in Computer Science and Engineering from the University of Notre Dame, Indiana, United States. He has worked for the National Electronics and Computer Technology Center on High Performance Computing (HPC) and Computational Grid. During 2002–2004, he cochaired the Asia-Pacific Advanced Network (APAN) Grid Working Group. In 2003, he shifted his research direction from HPC architecture to bioinformatics research, when he started working for BIOTEC, and constructed the ThaiSNP database. His main research interest is in developing algorithms and databases for analyzing various research projects on human genetic variation. He currently heads the Genome Institute biostatistics and informatics laboratory at BIOTEC. Prasit Palittapongarnpim, M.D., earned his medical degree from Mahidol University, Thailand, and his B.S. in Mathematics from Ramkumhang University, Thailand. He is a Fellow of the Royal College of Pediatricians of Thailand and also an Associate Professor in Microbiology at Mahidol University, where he has conducted research focusing on tuberculosis. While holding a Deputy Director position, he initiated the Bioinformatics research program at BIOTEC in 2002 and led the organization of the first InCoB conference in 2002. He is currently a Vice President of NSTDA.

Automated Bone Age Assessment of Older Children using the Radius.

The Digital Hand Atlas in Assessment of Skeletal Development is a large-scale Computer Aided Diagnosis (CAD) project for automating the process of grading Skeletal Development of children from 0-18 years of age. It includes a complete collection of 1,400 normal hand X-rays of children between the ages of 0-18 years of age. Bone Age Assessment is used as an index of skeletal development for detection of growth pathologies that can be related to endocrine, malnutrition and other disease types. Previous work at the Image Processing and Informatics Lab (IPILab) allowed the bone age CAD algorithm to accurately assess bone age of children from 1 to 16 (male) or 14 (female) years of age using the Phalanges as well as the Carpal Bones. At the older ages (16(male) or 14(female) -19 years of age) the Phalanges as well as the Carpal Bones are fully developed and do not provide well-defined features for accurate bone age assessment. Therefore integration of the Radius Bone as a region of interest (ROI) is greatly needed and will significantly improve the ability to accurately assess the bone age of older children. Preliminary studies show that an integrated Bone Age CAD that utilizes the Phalanges, Carpal Bones and Radius forms a robust method for automatic bone age assessment throughout the entire age range (1-19 years of age).

Medical Informatics in Morocco: Casablanca Medical Informatics Laboratory

In 2005, Medical Informatics Laboratory (CMIL) became an independent research unit within the Faculty of Medicine and Pharmacy of Casablanca. CMIL is currently run by three persons (a university professor, a data processing specialist and a pedagogical assistant). The objectives of CMIL are to promote research and develop quality in the field of biomedical data processing and health, and integrate new technologies into medical education and biostatistics. It has four units: Telehealth Unit, Network Unit, Biostatistics Unit, Medical data processing Unit. The present article seeks to give a comprehensive account of Casablanca Medical informatics laboratory (CMIL) activities. For ease of exposition, the article consists of four sections: Section I discusses the background of CMIL; section II is devoted to educational activities; section III addresses professional activities; and section IV lists projects that CMIL is involved in. Since its creation, CMIL has been involved in a number of national and international projects, which have a bearing on Telemedicine applications, E-learning skills and data management in medical studies in Morocco. It is our belief that the skills and knowledge gained in the past few years would certainly enrich our research activities, and improve the situation of research in Medical informatics in Morocco.

Developmental informatics at IIT Bombay

IIT Bombay's Developmental Informatics Lab is a cross disciplinary group consisting of 6 faculty, 30 research staff and several students. The lab is working towards increasing access to information -- through the use of internet and communication technologies -- to communities in the developing world especially rural and small town India. The lab is supported by Indian Government funding sources as well as corporate and multi-lateral agencies to solve technical problems in local communities in sustainable ways. This paper focuses on two mature projects of the lab -- one caters to Indian farmers while another helps with the education of tribal populations.

Doc’UMVF: Two search tools to provide quality-controlled teaching resources in French to students and teachers

The UMVF project is a federation of medical teaching resources covering 32 medical schools in France. Today, the indexing of these resources is carried out manually by the CISMeF team at the University Hospital of Rouen. This indexing is based on MeSH thesaurus. We use a subset of SCORM metadata standard. This choice was defined in collaboration with the French Medical Virtual University consortium (French acronym: UMVF). Currently, with the UMVF searching tool (called Doc’UMVF), medical students can reach more than 3300 resources useful in their curriculum. Doc’UMVF is developed in close collaboration between the medical informatics laboratories of Rennes and Rouen. In this paper we present two complementary searching tools based on different methods and which are integrated and used to improve both the relevance and the coverage rate of the answers. A specific searching module has been built to retrieve specific resources concerning the National Medical Exam ENC (“Examen National Classant”) is also available. Nevertheless, due to lack of time, numerous resources are not yet indexed. Therefore we have decided to use also automatic indexing method (Nomindex). This approach will be improved by further research works, resulting from Rouen and Geneva teams. After having built a searching meta-motor, our objective is to develop a meta-tool intended to index the whole set of digital pedagogical resources produced by the UMVF framework. This manual re-indexing will be carried out only for the most important resources (national references), with a more or less fine granularity.

A HIPAA-Compliant Architecture for Securing Clinical Images

The Health Insurance Portability and Accountability Act (HIPAA, instituted April 2003) Security Standards mandate health institutions to protect health information against unauthorized use or disclosure. One approach to addressing this mandate is by utilizing user access control and generating audit trails of the various authorized as well as unauthorized user access of health data. Although most current clinical image systems [e.g., picture archiving and communication system (PACS)] have components that generate log files for application debugging purposes, there is a lack of methodology to obtain and synthesize the pertinent data from the large volumes of log data generated by these multiple components within a PACS. We have designed a HIPAA-compliant architecture specifically for tracking and auditing the image workflow of clinical imaging systems such as PACS. As an initial first step, we developed HIPAA-compliant auditing system (H-CAS) based on parts of this HIPAA-compliant architecture. H-CAS was implemented within a test-bed PACS simulator located in the Image Processing and Informatics lab at the University of Southern California. Evaluation scenarios were developed where different user types performed legal and illegal access of PACS image data within each of the different components in the PACS simulator. Results were based on whether the scenarios of unauthorized access were correctly identified and documented as well as on normal operational activity. Integration and implementation pitfalls were also noted and included.

A Structured Interface to the Object-Oriented Genomics Unified Schema for XML-Formatted Data

Data management systems are fast becoming required components in many biology laboratories as the role of computer-based information grows. Although the need for data management systems is on the rise, their inherent complexities can deter the full and routine use of their computational capabilities. The significant undertaking to implement a capable production system can be reduced in part by adapting an established data management system. In such a way, we are leveraging the Genomics Unified Schema (GUS) developed at the Computational Biology and Informatics Laboratory at the University of Pennsylvania as a foundation for managing and analysing DNA sequence data in centromere research projects around Arabidopsis thaliana and related species. Because GUS provides a core schema that includes support for genome sequences, mRNA and its expression, and annotated chromosomes, it is ideal for synthesising a variety of parameters to analyse these repetitive and highly dynamic portions of the genome. Despite this, production-strength data management frameworks are complex, requiring dedicated efforts to adapt and maintain. The work reported in this article addresses one component of such an effort, namely the pivotal task of marshalling data from various sources into GUS. In order to harness GUS for our project, and motivated by efficiency needs, we developed a structured framework for transferring data into GUS from outside sources. This technology is embodied in a GUS object-layer processor, XMLGUS. XMLGUS facilitates incorporating data into GUS by (i) formulating an XML interface that includes relational database key constraint definitions, (ii) regularising traversal through that XML, (iii) realising automatic processing of the XML with database key constraints and (iv) allowing for special processing of input data within the framework for automated processing. The application of XMLGUS to production pipeline processing for a sequencing project and inputting the Arabidopsis genome into GUS is discussed. XMLGUS is available from the Flora website (http://flora.ittc.ku.edu/).

Medical image security in a HIPAA mandated PACS environment

Medical image security is an important issue when digital images and their pertinent patient information are transmitted across public networks. Mandates for ensuring health data security have been issued by the federal government such as Health Insurance Portability and Accountability Act (HIPAA), where healthcare institutions are obliged to take appropriate measures to ensure that patient information is only provided to people who have a professional need. Guidelines, such as digital imaging and communication in medicine (DICOM) standards that deal with security issues, continue to be published by organizing bodies in healthcare. However, there are many differences in implementation especially for an integrated system like picture archiving and communication system (PACS), and the infrastructure to deploy these security standards is often lacking. Over the past 6 years, members in the Image Processing and Informatics Laboratory, Childrens Hospital, Los Angeles/University of Southern California, have actively researched image security issues related to PACS and teleradiology. The paper summarizes our previous work and presents an approach to further research on the digital envelope (DE) concept that provides image integrity and security assurance in addition to conventional network security protection. The DE, including the digital signature (DS) of the image as well as encrypted patient information from the DICOM image header, can be embedded in the background area of the image as an invisible permanent watermark. The paper outlines the systematic development, evaluation and deployment of the DE method in a PACS environment. We have also proposed a dedicated PACS security server that will act as an image authority to check and certify the image origin and integrity upon request by a user, and meanwhile act also as a secure DICOM gateway to the outside connections and a PACS operation monitor for HIPAA supporting information.

Electronic imaging and clinical implementation: work group approach at Mayo Clinic, Rochester.

Electronic imaging clinical implementation strategies and principles need to be developed as we move toward replacement of film-based radiology practices. During an 8-month period (1998 to 1999), an Electronic Imaging Clinical Implementation Work Group (EICIWG) was formed from sections of our department: Informatics Lab, Finance Committee, Management Section, Regional Practice Group, as well as several organ and image modality sections of the Department of Diagnostic Radiology. This group was formed to study and implement policies and strategies regarding implementation of electronic imaging into our practice. The following clinical practice issues were identified as key focus areas: (1) optimal electronic worklist organization; (2) how and when to link images with reports; (3) how to redistribute technical and professional relative value units (RVU); (4) how to facilitate future practice changes within our department regarding physical location and work redistribution; and (5) how to integrate off-campus imaging into on-campus workflow. The EICIWG divided their efforts into two phases. Phase I consisted of Fact finding and review of current practice patterns and current economic models, as well as radiology consulting needs. Phase II involved the development of recommendations, policies, and strategies for reengineering the radiology department to maintain current practice goals and use electronic imaging to improve practice patterns. The EICIWG concluded that electronic images should only be released with a formal report, except in emergent situations. Electronic worklists should support and maintain the physical presence of radiologists in critical areas and direct imaging to targeted subspecialists when possible. Case tools should be developed and used in radiology and hospital information systems (RIS/HIS) to monitor a number of parameters, including professional and technical RVU data. As communication standards improve, proper staffing models must be developed to facilitate electronic on-campus and off-campus consultation.

Transfer of programs from LISP to BCPL environments: An experiment: Dan Stroemberg and Peter Fritzon: Informatics Laboratory, Linkoeping University, Linkoeping, March 1980

Transfer of programs from LISP to BCPL environments: An experiment: Dan Stroemberg and Peter Fritzon: Informatics Laboratory, Linkoeping University, Linkoeping, March 1980

Experiences from a program manipulation system: Anders Haraldsson: Informatics Laboratory, Linkoeping University, Linkoeping, July 1980

Experiences from a program manipulation system: Anders Haraldsson: Informatics Laboratory, Linkoeping University, Linkoeping, July 1980

Self-description and reproduction in distributed programming systems: Erik Sandewall: Informatics Laboratory, Linkoeping University, Linkoeping, August 1979

Self-description and reproduction in distributed programming systems: Erik Sandewall: Informatics Laboratory, Linkoeping University, Linkoeping, August 1979