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At least 1,189 records · Page 66Linked to original sources
PubMed2005

Mega2: data-handling for facilitating genetic linkage and association analyses.

UNLABELLED: Mega2, the manipulation environment for genetic analysis, transparently allows users to process genetic data for family-based or case/control studies accurately and efficiently. In addition to data validation checks, Mega2 provides analysis setup capabilities for a broad choice of commonly used genetic analysis programs, including SimWalk2, ASPEX, GeneHunter, SLINK, SIMULATE, S.A.G.E., SOLAR, Vitesse, Allegro, PREST, PAP, Loki, Merlin and MENDEL. AVAILABILITY: http://watson.hgen.pitt.edu/register/

Chromosome Mapping↗
PubMed2006

Adapters, shims, and glue--service interoperability for in silico experiments.

MOTIVATION: Computationally, in silico experiments in biology are workflows describing the collaboration of people, data and methods. The Grid and Web services are proposed to be the next generation infrastructure supporting the deployment of bioinformatics workflows. But the growing number of autonomous and heterogeneous services pose challenges to the used middleware w.r.t. composition, i.e. discovery and interoperability of services required within in silico experiments. In the IRIS project, we handle the problem of service interoperability by a semi-automatic procedure for identifying and placing customizable adapters into workflows built by service composition. RESULTS: We show the effectiveness and robustness of the software-aided composition procedure by a case study in the field of life science. In this study we combine different database services with different analysis services with the objective of discovering required adapters. Our experiments show that we can identify relevant adapters with high precision and recall.

Computational Biology↗
PubMed2003

A contextual role-based access control authorization model for electronic patient record.

The design of proper models for authorization and access control for electronic patient record (EPR) is essential to a wide scale use of EPR in large health organizations. In this paper, we propose a contextual role-based access control authorization model aiming to increase the patient privacy and the confidentiality of patient data, whereas being flexible enough to consider specific cases. This model regulates user's access to EPR based on organizational roles. It supports a role-tree hierarchy with authorization inheritance; positive and negative authorizations; static and dynamic separation of duties based on weak and strong role conflicts. Contextual authorizations use environmental information available at access time, like user/patient relationship, in order to decide whether a user is allowed to access an EPR resource. This enables the specification of a more flexible and precise authorization policy, where permission is granted or denied according to the right and the need of the user to carry out a particular job function.

Algorithms↗
PubMed2004

A smart-card-enabled privacy preserving E-prescription system.

Within the overall context of protection of health care information, privacy of prescription data needs special treatment. First, the involvement of diverse parties, especially nonmedical parties in the process of drug prescription complicates the protection of prescription data. Second, both patients and doctors have privacy stakes in prescription, and their privacy should be equally protected. Third, the following facts determine that prescription should not be processed in a truly anonymous manner: certain involved parties conduct useful research on the basis of aggregation of prescription data that are linkable with respect to either the patients or the doctors; prescription data has to be identifiable in some extreme circumstances, e.g., under the court order for inspection and assign liability. In this paper, we propose an e-prescription system to address issues pertaining to the privacy protection in the process of drug prescription. In our system, patients' smart cards play an important role. For one thing, the smart cards are implemented to be portable repositories carrying up-to-date personal medical records and insurance information, providing doctors instant data access crucial to the process of diagnosis and prescription. For the other, with the secret signing key being stored inside, the smart card enables the patient to sign electronically the prescription pad, declaring his acceptance of the prescription. To make the system more realistic, we identify the needs for a patient to delegate his signing capability to other people so as to protect the privacy of information housed on his card. A strong proxy signature scheme achieving technologically mutual agreements on the delegation is proposed to implement the delegation functionality.

Algorithms↗
PubMed2004

Towards cooperative frameworks for modeling and integrating biological processes knowledge.

Data organization has become a strategic target for biologists due to the increasing volume of genomic data available for them. For this purpose, we need a complete knowledge model for representing biological system. In this paper, we deal with both processes for the creation and integration of shareable, reusable domain models within biology, which is a critical issue. In particular, this work introduces a new cooperative development approach for biology ontologies. This approach is based on the integration of the ontologies supplied by different human experts. Two experiments in biological domains are presented and their results discussed.

Artificial Intelligence↗
PubMed2006

The Gaggle: an open-source software system for integrating bioinformatics software and data sources.

BACKGROUND: Systems biologists work with many kinds of data, from many different sources, using a variety of software tools. Each of these tools typically excels at one type of analysis, such as of microarrays, of metabolic networks and of predicted protein structure. A crucial challenge is to combine the capabilities of these (and other forthcoming) data resources and tools to create a data exploration and analysis environment that does justice to the variety and complexity of systems biology data sets. A solution to this problem should recognize that data types, formats and software in this high throughput age of biology are constantly changing. RESULTS: In this paper we describe the Gaggle -a simple, open-source Java software environment that helps to solve the problem of software and database integration. Guided by the classic software engineering strategy of separation of concerns and a policy of semantic flexibility, it integrates existing popular programs and web resources into a user-friendly, easily-extended environment. We demonstrate that four simple data types (names, matrices, networks, and associative arrays) are sufficient to bring together diverse databases and software. We highlight some capabilities of the Gaggle with an exploration of Helicobacter pylori pathogenesis genes, in which we identify a putative ricin-like protein -a discovery made possible by simultaneous data exploration using a wide range of publicly available data and a variety of popular bioinformatics software tools. CONCLUSION: We have integrated diverse databases (for example, KEGG, BioCyc, String) and software (Cytoscape, DataMatrixViewer, R statistical environment, and TIGR Microarray Expression Viewer). Through this loose coupling of diverse software and databases the Gaggle enables simultaneous exploration of experimental data (mRNA and protein abundance, protein-protein and protein-DNA interactions), functional associations (operon, chromosomal proximity, phylogenetic pattern), metabolic pathways (KEGG) and Pubmed abstracts (STRING web resource), creating an exploratory environment useful to 'web browser and spreadsheet biologists', to statistically savvy computational biologists, and those in between. The Gaggle uses Java RMI and Java Web Start technologies and can be found at http://gaggle.systemsbiology.net.

Computational Biology↗
PubMed1998

Conceptual integration of information databases into an Intranet.

Large information systems handle massive volume of data stored in heterogeneous sources of information. Each server has its own model of concepts representation with regard to its aims. One of the main problems encountered by end-users when accessing different servers is to match their own viewpoint on biomedical concepts with their various representations that are made in the database servers. The aim of the project ARIANE is to provide end-users with easy-to-use and natural means to access and query heterogeneous information databases. The objectives of this research work consist in building a conceptual interface by means of the Internet technology inside an enterprise Intranet, and to propose a method to realize it. Moreover, this method provides designers of web sites with a powerful tool to manage them on the basis of an ontology of the biomedical domain. This method is based on the knowledge sources provided by the Unified Medical Language System project of the U.S. National Library of Medicine and exploits intensively the conceptual graphs theory.

Computer Communication Networks↗
PubMed1999

More space, more speed. Scanning technology and COLD help improve document imaging.

UNLABELLED: Children's Hospital Medical Center, Akron, Ohio PROBLEM: The 100-year-old-plus medical center needed a reliable, economical and easy-to-use document storage method that provided a long and secure archival life. SOLUTION: Children's adopted Hewlett-Packard magneto-optical jukeboxes and Optika software. RESULTS: Since the jukeboxes became operational in January 1998, Children's has maintained "24 x 7 availability" of its stored documents for up to 150 concurrent users without any downtime. KEYS TO SUCCESS: "We started implementation in the accounting department with patient billing, hospital general ledger, accounts payable and employee payroll, and the document imaging system has quickly gained acceptance in other departments as well."

Hospital Information Systems↗
PubMed2000

PACS and RIS: approaches to integration.

PACS and RIS have traditionally been discrete information systems with separate databases. Maintaining more than one database containing identical data sets creates the potential for outdated information being used in parallel with accurate information. Today, because of increased implementation of PACS and improved Web technology, this problem must be solved. Furthermore, as PACS technology is applied to areas outside radiology such database issues become more critical. Application of XML offers a cost-effective and workable solution to many of the thorniest problems that will likely become more prevalent in the post-Y2K era.

Database Management Systems↗
PubMed2000

Long term preservation of electronic health records. Recommendations in a large teaching hospital in Belgium.

Health records should be readily accessed by authorised persons for diagnosis, treatment and legal security purposes during patient's lifetime and thereafter for research and training purposes. Technology makes difficult the preservation of digital material, because of rapid changes in information media, hardware and software evolution, and because of the multiplicity of its location as well as the complexity of its environment. A committee in a large teaching hospital in Belgium, recommends two complementary approaches: (1) After a patient departure, all his health information should be managed by a unique organisation that would update regularly accesses to all data bases concerned by this patient. Health archives should be formatted using XML (Extensible Mark up Language) software family, and set on supports such as DVD-ROM, to be upgraded or updated when needed. This archive media is fast but not safe. (2) Computer output microfilm (COM) and scanners for non electronic data to be preserved appears to be also needed, as it is storage safe for at least 250 years and readable directly by eye. This archive media is safe but not fast.

Archives↗
PubMed2001

Data mining for on-line support of general practice.

Statistical relationships among symptoms, diagnoses and treatments can be inferred from large data-bases of health records. We investigate how these "empirical norms" can be utilized to improve the efficiency and quality assurance capability of on-line systems in General Practice medicine. Using a survey-based database of General Practice records, we assess hotlists (case sensitive menus) of diagnoses to speed data entry. We also explore norm violation as an indicator of poor quality in practice or data recording. We find that efficient hotlists of diagnoses can be generated from symptoms. Also, we find that less frequently used hypertension treatments are assessed as of a lower quality than more common ones. The results support the hypothesis that empirical norms have a role to play in improved General Practice systems.

Australia↗
PubMed2002

EDMS: what it was, is, and could be.

The decision to implement an Electronic Document Management System (EDMS) should not be made lightly. Such is the advice of a health are provider organization that pioneered the technology a decade ago. University Health Systems of Eastern Carolina's largest facility, Pitt County Memorial Hospital (PCMH), implemented an EDMS in February 1992 and converted to its current EDMS in December 1999. This article describes PCMH's transition from paper to automation, the many trials along the way, and the advantages an EDMS offers.

Electronic Data Processing↗
PubMed2002

Experiences with extracting structured patient data for use in clinical research.

Routinely collected patient data are often recorded as unstructured and ambiguous free text by physicians. These data are, however, also of interest to clinical researchers, for whom they must be clearly defined and preferably coded. We have developed an application to support physicians in recording patient data in a structured, yet expressive manner. The flexible domain-independent data representation and storage approach underlying the application made data extraction for research purposes very complex. The changes that we made to the representation and storage approach to facilitate extraction, without reducing expressiveness for data entry, are presented in this paper, together with the underlying principles of the data extraction tool that we created to enable data extraction for clinical research.

Biomedical Research↗
PubMed2004

Sending data to a central repository.

The Veterinary Medical DataBases (VMDB) has been collecting data from participating institutions for 40 years. We have recently started a program to collect clinical case data from not only veterinary schools but from veterinary practitioners as well. In so doing, we are using commonly accepted means of data representation and transmission. Thus, we use the Standard Nomenclature of Medicine (SNOMED) as a standard vocabulary language and Health Level 7 (HL 7) as a standard transmission protocol. We report on the planning and implementation of these standards and the problems encountered in their implementation.

Animal Diseases↗