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Security aspects of Grid-based digital mammography.

OBJECTIVES: The principal aim of the eDiaMoND project is to develop a prototype Grid infrastructure to support the needs of the breast care community. The prototype system is but one major deliverable of the project; the other is a blueprint document that describes how a system such as eDiaMoND might be deployed throughout the United Kingdom to support the NHS Breast Screening Programme. A key consideration of both the prototype and the blueprint is security. In this paper we address some of the generic security issues faced by projects such as eDiaMoND. We also indicate how these problems are being overcome within our project. METHODS: In order to fully understand the security issues faced by the project a review of current initiatives within the NHS was performed. The work of the NHS Information Authority was found to be particularly significant. Also reviewed was BS7799, the British Standard for the deployment of security systems and processes. Finally, modelling of the proposed prototype was performed using methods proposed by the e-Science Security Task Force, in particular the method proposed by Flechais and Sasse. RESULTS AND CONCLUSIONS: It is felt that the issues of security surrounding the eDiaMoND project are sufficiently generic that the eHealth community can consider and criticise the work described. It is hoped that this will enable the eHealth community to move forwards with a common agenda.

Access to Information↗

Information for chemical management. The approach of the International Register of Potentially Toxic Chemicals.

The International Register of Potentially Toxic Chemicals (IRPTC) chemical data bank system was developed with the view to covering all the sets of information needed for the identification of hazard and providing a useful tool for risk assessment. The IRPTC data bank has been conceived to allow countries to establish their own information management system for national chemical management and to serve a worldwide information exchange network. The electronic search facilities help to provide tailor made data sets to fit the information needs of the different groups and individuals. There is a great variety of information users, ranging from those dealing with the hazard assessment and risk management to the exposed workers and citizens concerned about the effects of the emissions from the smokestack of the neighbouring factory. The need for authoritative information is particularly crucial for developing countries which do not have the advanced technological means or resources to establish mainframe computing links with IRPTC. A personal computer version has therefore been developed to give these governments and institutions access to the same data at an extensively reduced cost.

Database Management Systems↗

Genome Information Broker (GIB): data retrieval and comparative analysis system for completed microbial genomes and more.

Genome Information Broker (GIB) is a powerful tool for the study of comparative genomics. GIB allows users to retrieve and display partial and/or whole genome sequences together with the relevant biological annotation. GIB has accumulated all the completed microbial genome and has recently been expanded to include Arabidopsis thaliana genome data from DDBJ/EMBL/GenBank. In the near future, hundreds of genome sequences will be determined. In order to handle such huge data, we have enhanced the GIB architecture by using XML, CORBA and distributed RDBs. We introduce the new GIB here. GIB is freely accessible at http://gib.genes.nig.ac.jp/.

Arabidopsis↗

Health information systems - past, present, future.

In 1984, Peter Reichertz gave a lecture on the past, present and future of hospital information systems. In the meantime, there has been a tremendous progress in medicine as well as in informatics. One important benefit of this progress is that our life expectancy is nowadays significantly higher than it would have been even some few decades ago. This progress, leading to aging societies, is of influence to the organization of health care and to the future development of its information systems. Twenty years later, referring to Peter Reichertz' lecture, but now considering health information systems (HIS), two questions are discussed: which were lines of development in health information systems from the past until today? What are consequences for health information systems in the future? The following lines of development for HIS were considered as important: (1) the shift from paper-based to computer-based processing and storage, as well as the increase of data in health care settings; (2) the shift from institution-centered departmental and, later, hospital information systems towards regional and global HIS; (3) the inclusion of patients and health consumers as HIS users, besides health care professionals and administrators; (4) the use of HIS data not only for patient care and administrative purposes, but also for health care planning as well as clinical and epidemiological research; (5) the shift from focusing mainly on technical HIS problems to those of change management as well as of strategic information management; (6) the shift from mainly alpha-numeric data in HIS to images and now also to data on the molecular level; (7) the steady increase of new technologies to be included, now starting to include ubiquitous computing environments and sensor-based technologies for health monitoring. As consequences for HIS in the future, first the need for institutional and (inter-) national HIS-strategies is seen, second the need to explore new (transinstitutional) HIS architectural styles, third the need for education in health informatics and/or biomedical informatics, including appropriate knowledge and skills on HIS. As these new HIS are urgently needed for reorganizing health care in an aging society, as last consequence the need for research around HIS is seen. Research should include the development and investigation of appropriate transinstitutional information system architectures, of adequate methods for strategic information management, of methods for modeling and evaluating HIS, the development and investigation of comprehensive electronic patient records, providing appropriate access for health care professionals as well as for patients, in the broad sense as described here, e.g. including home care and health monitoring facilities. Comparing the world in 1984 and in 2004, we have to recognize that we imperceptibly, stepwise arrived at a new world. HIS have become one of the most challenging and promising fields of research, education and practice for medical informatics, with significant benefits to medicine and health care in general.

Computer Systems↗

JXP4BIGI: a generalized, Java XML-based approach for biological information gathering and integration.

MOTIVATION: In the post-genomic era, biologists interested in systems biology often need to import data from public databases and construct their own system-specific or subject-oriented databases to support their complex analysis and knowledge discovery. To facilitate the analysis and data processing, customized and centralized databases are often created by extracting and integrating heterogeneous data retrieved from public databases. A generalized methodology for accessing, extracting, transforming and integrating the heterogeneous data is needed. RESULTS: This paper presents a new data integration approach named JXP4BIGI (Java XML Page for Biological Information Gathering and Integration). The approach provides a system-independent framework, which generalizes and streamlines the steps of accessing, extracting, transforming and integrating the data retrieved from heterogeneous data sources to build a customized data warehouse. It allows the data integrator of a biological database to define the desired bio-entities in XML templates (or Java XML pages), and use embedded extended SQL statements to extract structured, semi-structured and unstructured data from public databases. By running the templates in the JXP4BIGI framework and using a number of generalized wrappers, the required data from public databases can be efficiently extracted and integrated to construct the bio-entities in the XML format without having to hard-code the extraction logics for different data sources. The constructed XML bio-entities can then be imported into either a relational database system or a native XML database system to build a biological data warehouse. AVAILABILITY: JXP4BIGI has been integrated and tested in conjunction with the IKBAR system (http://www.ikbar.org/) in two integration efforts to collect and integrate data for about 200 human genes related to cell death from HUGO, Ensembl, and SWISS-PROT (Bairoch and Apweiler, 2000), and about 700 Drosophila genes from FlyBase (FlyBase Consortium, 2002). The integrated data has been used in comparative genomic analysis of x-ray induced cell death. Also, as explained later, JXP4BIGI is a middleware and framework to be integrated with biological database applications, and cannot run as a stand-alone software for end users. For demonstration purposes, a demonstration version is accessible at (http://www.ikbar.org/jxp4bigi/demo.html).

Database Management Systems↗

Saturated BLAST: an automated multiple intermediate sequence search used to detect distant homology.

MOTIVATION: Two proteins can have a similar 3-dimensional structure and biological function, but have sequences sufficiently different that traditional protein sequence comparison algorithms do not identify their relationship. The desire to identify such relations has led to the development of more sensitive sequence alignment strategies. One such strategy is the Intermediate Sequence Search (ISS), which connects two proteins through one or more intermediate sequences. In its brute-force implementation, ISS is a strategy that repetitively uses the results of the previous query as new search seeds, making it time-consuming and difficult to analyze. RESULTS: Saturated BLAST is a package that performs ISS in an efficient and automated manner. It was developed using Perl and Perl/Tk and implemented on the LINUX operating system. Starting with a protein sequence, Saturated BLAST runs a BLAST search and identifies representative sequences for the next generation of searches. The procedure is run until convergence or until some predefined criteria are met. Saturated BLAST has a friendly graphic user interface, a built-in BLAST result parser, several multiple alignment tools, clustering algorithms and various filters for the elimination of false positives, thereby providing an easy way to edit, visualize, analyze, monitor and control the search. Besides detecting remote homologies, Saturated BLAST can be used to maintain protein family databases and to search for new genes in genomic databases.

Algorithms↗

Representing genetic sequence data for pharmacogenomics: an evolutionary approach using ontological and relational models.

MOTIVATION: The information model chosen to store biological data affects the types of queries possible, database performance, and difficulty in updating that information model. Genetic sequence data for pharmacogenetics studies can be complex, and the best information model to use may change over time. As experimental and analytical methods change, and as biological knowledge advances, the data storage requirements and types of queries needed may also change. RESULTS: We developed a model for genetic sequence and polymorphism data, and used XML Schema to specify the elements and attributes required for this model. We implemented this model as an ontology in a frame-based representation and as a relational model in a database system. We collected genetic data from two pharmacogenetics resequencing studies, and formulated queries useful for analysing these data. We compared the ontology and relational models in terms of query complexity, performance, and difficulty in changing the information model. Our results demonstrate benefits of evolving the schema for storing pharmacogenetics data: ontologies perform well in early design stages as the information model changes rapidly and simplify query formulation, while relational models offer improved query speed once the information model and types of queries needed stabilize.

Algorithms↗

EGene: a configurable pipeline generation system for automated sequence analysis.

UNLABELLED: EGene is a generic, flexible and modular pipeline generation system that makes pipeline construction a modular job. EGene allows for third-party programs to be used and integrated according to the needs of distinct projects and without any previous programming or formal language experience being required. EGene comes with CoEd, a visual tool to facilitate pipeline construction and documentation. A series of components to build pipelines for sequence processing is provided. AVAILABILITY: http://www.lbm.fmvz.usp.br/egene/ CONTACT: alan@ime.usp.br; argruber@usp.br SUPPLEMENTARY INFORMATION: http://www.lbm.fmvz.usp.br/egene/

Chromosome Mapping↗

HESAS: HERVs Expression and Structure Analysis System.

SUMMARY: HESAS (HERVs Expression and Structure Analysis System) database was developed to understand the human endogenous retroviruses (HERVs) that have an effect on the expression of human functional genes. The database products are generated by the exon-based expressed sequence tag clustering and reconstructing of partial HERV structures that result from various mutations during primate evolution. The expression types were classified according to the existence of splicing, transcriptional start and polyadenylation signal sites. The database currently contains HERV information on 26,981 human genes of exon-intron structure. The HERV elements were inserted into 17,317 of these genes and linked to expression with 898 genes. AVAILABILITY: http://www.primate.or.kr/HESAS CONTACT: khs307@pusan.ac.kr.

Algorithms↗

[Computer program for improved diagnostic coding in ophthalmology based on the expanded ICD 10].

BACKGROUND: The coding of ophthalmological diagnoses is a long-standing problem that has recently been highlighted by the planned introduction of ICD 10. METHODS: Using an alphanumerical classification system for the first time, ICD 10 offers the space needed for necessary expansion without leading once again to dislocations in the numbering system. The FoxPro 2.5 database system was used to create a program based on an expanded ICD 10 that can be applied from DOS and Windows. RESULTS: ICD 10 was expanded by the addition of a numerical fifth digit, thus increasing the number of classifiable ophthalmological disorders by a factor of 4.2 from 390 to 1635. The new program greatly facilitates the handling of this substantial amount of data. CONCLUSIONS: The enhanced diagnosis coding achieved with the expanded ICD 10 permits nosologically exact statistics to be kept for use as a basis for further scientific work.

Data Display↗

Functional and user requirements for IMACS.

An Image Management, Archiving and Communication System (IMACS) should integrate all imaging modalities in a diagnostic radiology department. In order to obtain this integration, manufacturers of diagnostic imaging modalities must follow the established standards for communication protocols and image formats. To gain acceptance, IMACS must result in one or more of the following: cost savings, improved efficiency or added diagnostic information. The increased possibilities for image processing should result in a reduced number of rejects and an improved and more uniform image quality. The IMACS should be interconnectable with a range of different Hospital Information Systems (HIS) and Radiological Information Systems (RIS). Interconnections with the HIS and the RIS are mandatory in order to fulfil the specified requirements with regard to access times and functionality.

Computer Systems↗

A 32 key keyboard for the HP PDMS.

The keyboard remains the primary human interface device for existing patient data management systems. The standard bedside keyboard for the Hewlett-Packard PDMS has 16 keys which are used for both numeric data entry and multiple functions, accessed by shift key combinations. We have designed and constructed a 32 key keyboard which speeds single keystroke access to all PDMS functions. The new keyboard is backwards compatible and requires no PDMS software changes. A 32 key keyboard offers many advantages for use with the HP PDMS. The device presented is backwards compatible with the vendor's keyboard and requires no software changes. This keyboard could serve as an updated functional replacement for thousands of keyboards now in use.

Computer Systems↗

A task framework for the web interface W2H.

SUMMARY: The W3H task framework allows the execution of compound jobs utilizing the description of work and data flows in a heterogeneous bioinformatics environment using meta-data information. By means of these descriptions, the task system can schedule the necessary execution of applications available in the environment, depending on rules specified in the meta-data. By integrating this task framework into the publicly available web interface W2H, similarly based on meta-data, web access and data management are immediately available for each task description. Authors of task descriptions can base their work on the underlying classes and objects to be able to describe dependency rules between previously independent applications. The result of a compound task is given as XML data that is translated according to XSLT data into web pages or plain text to report the result of the task to the user. AVAILABILITY: Within the HUSAR environment at DKFZ http://genome.dkfz-heidelberg.de/

Database Management Systems↗

HOWDY: an integrated database system for human genome research.

HOWDY is an integrated database system for accessing and analyzing human genomic information (http://www-alis.tokyo.jst.go.jp/HOWDY/). HOWDY stores information about relationships between genetic objects and the data extracted from a number of databases. HOWDY consists of an Internet accessible user interface that allows thorough searching of the human genomic databases using the gene symbols and their aliases. It also permits flexible editing of the sequence data. The database can be searched using simple words and the search can be restricted to a specific cytogenetic location. Linear maps displaying markers and genes on contig sequences are available, from which an object can be chosen. Any search starting point identifies all the information matching the query. HOWDY provides a convenient search environment of human genomic data for scientists unsure which database is most appropriate for their search.

Chromosome Mapping↗

Implementation of a database on drugs into a university hospital Intranet.

Several databases on drugs have been developed worldwide for drug information functions whose sources are now electronically available. Our objective was to implement one of them in our University hospitals information system. Thériaque is a database which contains information on all the drugs available in France. Before its implementation we modeled its content (chemical classes, active components, excipients, indications, contra-indications, side effects, and so on) following an object-oriented method. From this model we designed dynamic HTML pages according to the Microsoft's Internet Database Connector (IDC) technics. This allowed a fast implementation and does not imply to port a client application on the thousands of workstations over the network of the University hospitals. This interface provides end-users with an easy-to-use and natural way to access information related to drugs in an Intranet environment.

Computer Communication Networks↗

Tracker: continuous HMMER and BLAST searching.

SUMMARY: Tracker is a web-based email alert system for monitoring protein database searches using HMMER and Blast-P, nucleotide searches using Blast-N and literature searches of the PubMed database. Users submit searches via a web-based interface. Searches are saved and run against updated databases to alert users about new information. If there are new results from the saved searches, users will be notified by email and will then be able to access results and link to additional information on the NCBI website. Tracker supports Boolean AND/OR operations on HMMER and BLASTP result sets to allow users to broaden or narrow protein searches. AVAILABILITY: The server is located at http://jay.bioinformatics.ku.edu/tracker/index.html. A distribution package including detailed installation procedure is freely available from http://jay.bioinformatics.ku.edu/download/tracker/.

Database Management Systems↗

Adding some SPICE to DAS.

UNLABELLED: The distributed annotation system (DAS) defines a communication protocol used to exchange biological annotations. It is motivated by the idea that annotations should not be provided by single centralized databases but instead be spread over multiple sites. Data distribution, performed by DAS servers, is separated from visualization, which is carried out by DAS clients. The original DAS protocol was designed to serve annotation of genomic sequences. We have extended the protocol to be applicable to macromolecular structures. Here we present SPICE, a new DAS client that can be used to visualize protein sequence and structure annotations. AVAILABILITY: http://www.efamily.org.uk/software/dasclients/spice/

Algorithms↗

Reengineering a database for clinical trials management: lessons for system architects.

This paper describes the process of enhancing Trial/DB, a database system for clinical studies management. The system's enhancements have been driven by the need to maximize the effectiveness of developer personnel in supporting numerous and diverse users, of study designers in setting up new studies, and of administrators in managing ongoing studies. Trial/DB was originally designed to work over a local area network within a single institution, and basic architectural changes were necessary to make it work over the Internet efficiently as well as securely. Further, as its use spread to diverse communities of users, changes were made to let the processes of study design and project management adapt to the working styles of the principal investigators and administrators for each study. The lessons learned in the process should prove instructive for system architects as well as managers of electronic patient record systems.

Clinical Trials as Topic↗