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PubMedDate not supplied

Potential use of extensible markup language for radiology reporting: a tutorial.

One of the main goals of radiology is to communicate imaging information to aid in patient management. Information standards can facilitate communication and help realize this goal. Extensible Markup Language (XML) is a new information transmission standard that was developed to meet the growing need for robust, large-scale World Wide Web applications. XML notation provides a compact document representation scheme that allows radiology reports to be transmitted over the Web as universally understandable, self-defining documents. XML documents can include a report-specific document type definition (DTD) that defines the allowable data fields and values. XML may also be used to generate data entry forms for radiology reporting and help physicians improve the efficiency of the reporting process. XML documents can be used to store reporting results directly, thus allowing pertinent data to be shared on the Web. An XML-based approach can allow users to link information to entities outside the information systems of a given institution. XML-based methods and applications have the potential to promote development of robust radiology reporting systems and integration with broader, enterprise-wide information systems.

Databases as Topic↗
PubMed2006

EGassembler: online bioinformatics service for large-scale processing, clustering and assembling ESTs and genomic DNA fragments.

Expressed sequence tag (EST) sequencing has proven to be an economically feasible alternative for gene discovery in species lacking a draft genome sequence. Ongoing large-scale EST sequencing projects feel the need for bioinformatics tools to facilitate uniform EST handling. This brings about a renewed importance for a universal tool for processing and functional annotation of large sets of ESTs. EGassembler (http://egassembler.hgc.jp/) is a web server, which provides an automated as well as a user-customized analysis tool for cleaning, repeat masking, vector trimming, organelle masking, clustering and assembling of ESTs and genomic fragments. The web server is publicly available and provides the community a unique all-in-one online application web service for large-scale ESTs and genomic DNA clustering and assembling. Running on a Sun Fire 15K supercomputer, a significantly large volume of data can be processed in a short period of time. The results can be used to functionally annotate genes, to facilitate splice alignment analysis, to link the transcripts to genetic and physical maps, design microarray chips, to perform transcriptome analysis and to map to KEGG metabolic pathways. The service provides an excellent bioinformatics tool to research groups in wet-lab as well as an all-in-one-tool for sequence handling to bioinformatics researchers.

Computational Biology↗
PubMed2004

ESTminer: a Web interface for mining EST contig and cluster databases.

UNLABELLED: ESTminer is a Web application and database schema for interactive mining of expressed sequence tag (EST) contig and cluster datasets. The Web interface contains a query frame that allows the selection of contigs/clusters with specific cDNA library makeup or a threshold number of members. The results are displayed as color-coded tree nodes, where the color indicates the fractional size of each cDNA library component. The nodes are expandable, revealing library statistics as well as EST or contig members, with links to sequence data, GenBank records or user configurable links. Also, the interface allows 'queries within queries' where the result set of a query is further filtered by the subsequent query. AVAILABILITY: ESTminer is implemented in Java/JSP and the package, including MySQL and Oracle schema creation scripts, is available from http://cggc.agtec.uga.edu/Data/download.asp CONTACT: agingle@uga.edu.

Algorithms↗
PubMed2002

The semantic metadatabase (SEMEDA): ontology based integration of federated molecular biological data sources.

A system for "intelligent" semantic integration and querying of federated databases is being implemented by using three main components: A component which enables SQL access to integrated databases by database federation (MARGBench), an ontology based semantic metadatabase (SEMEDA) and an ontology based query interface (SEMEDA-query). In this publication we explain and demonstrate the principles, architecture and the use of SEMEDA. Since SEMEDA is implemented as 3 tiered web application database providers can enter all relevant semantic and technical information about their databases by themselves via a web browser. SEMEDA' s collaborative ontology editing feature is not restricted to database integration, and might also be useful for ongoing ontology developments, such as the "Gene Ontology" [2]. SEMEDA can be found at http://www-bm.cs.uni-magdeburg.de/semeda/. We explain how this ontologically structured information can be used for semantic database integration. In addition, requirements to ontologies for molecular biological database integration are discussed and relevant existing ontologies are evaluated. We further discuss how ontologies and structured knowledge sources can be used in SEMEDA and whether they can be merged supplemented or updated to meet the requirements for semantic database integration.

Databases, Genetic↗
PubMed2006

UniFrac--an online tool for comparing microbial community diversity in a phylogenetic context.

BACKGROUND: Moving beyond pairwise significance tests to compare many microbial communities simultaneously is critical for understanding large-scale trends in microbial ecology and community assembly. Techniques that allow microbial communities to be compared in a phylogenetic context are rapidly gaining acceptance, but the widespread application of these techniques has been hindered by the difficulty of performing the analyses. RESULTS: We introduce UniFrac, a web application available at http://bmf.colorado.edu/unifrac, that allows several phylogenetic tests for differences among communities to be easily applied and interpreted. We demonstrate the use of UniFrac to cluster multiple environments, and to test which environments are significantly different. We show that analysis of previously published sequences from the Columbia river, its estuary, and the adjacent coastal ocean using the UniFrac interface provided insights that were not apparent from the initial data analysis, which used other commonly employed techniques to compare the communities. CONCLUSION: UniFrac provides easy access to powerful multivariate techniques for comparing microbial communities in a phylogenetic context. We thus expect that it will provide a completely new picture of many microbial interactions and processes in both environmental and medical contexts.

Bacteria↗
PubMed2005

BioContrasts: extracting and exploiting protein-protein contrastive relations from biomedical literature.

MOTIVATION: Contrasts are useful conceptual vehicles for learning processes and exploratory research of the unknown. For example, contrastive information between proteins can reveal what similarities, divergences and relations there are of the two proteins, leading to invaluable insights for better understanding about the proteins. Such contrastive information are found to be reported in the biomedical literature. However, there have been no reported attempts in current biomedical text mining work that systematically extract and present such useful contrastive information from the literature for exploitation. RESULTS: Our BioContrasts system extracts protein-protein contrastive information from MEDLINE abstracts and presents the information to biologists in a web-application for exploitation. Contrastive information are identified in the text abstracts with contrastive negation patterns such as 'A but not B'. A total of 799 169 pairs of contrastive expressions were successfully extracted from 2.5 million MEDLINE abstracts. Using grounding of contrastive protein names to Swiss-Prot entries, we were able to produce 41 471 pieces of contrasts between Swiss-Prot protein entries. These contrastive pieces of information are then presented via a user-friendly interactive web portal that can be exploited for applications such as the refinement of biological pathways. AVAILABILITY: BioContrasts can be accessed at http://biocontrasts.i2r.a-star.edu.sg. It is also mirrored at http://biocontrasts.biopathway.org. SUPPLEMENTARY INFORMATION: Supplementary materials are available at Bioinformatics online.

Artificial Intelligence↗
PubMed2003

A full XML-based approach to creating hypermedia learning modules in web-based environments: application to a pathology course.

Nowadays, web-based learning services are a key topic in the pedagogical and learning strategies of universities. While organisational and teaching requirements of the learning environment are being evaluated, technical specifications are emerging, enabling educators to build advanced "units of learning". Changes, however, take a long time and cost-effective solutions have to be found to involve our institutions in such actions. In this paper, we present a model of the components of a course. We detail the method followed to implement this model in hypermedia modules with a viewer that can be played on line or from a CD-ROM. The XML technology has been used to implement all the data structures and a client-side architecture has been designed to build a course viewer. Standards of description of content (such as Dublin Core and DocBook) have been integrated into the data structures. This tool has been populated with data from a pathology course and supports other medical contents. The choice of the architecture and the usefulness of the programming tools are discussed. The means of migrating towards a server-side application are presented.

CD-ROM↗
PubMed2004

Improved prediction of protein-protein binding sites using a support vector machines approach.

MOTIVATION: Structural genomics projects are beginning to produce protein structures with unknown function, therefore, accurate, automated predictors of protein function are required if all these structures are to be properly annotated in reasonable time. Identifying the interface between two interacting proteins provides important clues to the function of a protein and can reduce the search space required by docking algorithms to predict the structures of complexes. RESULTS: We have combined a support vector machine (SVM) approach with surface patch analysis to predict protein-protein binding sites. Using a leave-one-out cross-validation procedure, we were able to successfully predict the location of the binding site on 76% of our dataset made up of proteins with both transient and obligate interfaces. With heterogeneous cross-validation, where we trained the SVM on transient complexes to predict on obligate complexes (and vice versa), we still achieved comparable success rates to the leave-one-out cross-validation suggesting that sufficient properties are shared between transient and obligate interfaces. AVAILABILITY: A web application based on the method can be found at http://www.bioinformatics.leeds.ac.uk/ppi_pred. The dataset of 180 proteins used in this study is also available via the same web site. CONTACT: westhead@bmb.leeds.ac.uk SUPPLEMENTARY INFORMATION: http://www.bioinformatics.leeds.ac.uk/ppi-pred/supp-material.

Algorithms↗
PubMed2001

The Internet as a source of information on breast augmentation.

The Internet was evaluated as a source of information for the layperson on the topic of breast augmentation. Three commonly used search engines (Excite, AOL, and Yahoo) were employed using the term "breast augmentation." These sites were then evaluated by each of three experienced plastic surgeons for their quality and content. Separately, 17 health Web sites were identified as authoritative by means of recommendation in lay publications. Each "supersite" was accessed, and its search engine was used. The top 10 hits for "breast augmentation" on each site were then evaluated by the senior author for content (Matthews). We found the majority of sites identified by the general search engines (AOL, Excite, Yahoo) to be physician Web sites. Forty-one unique sites were found that applied to the topic. Four of the "hits" did not actually apply to the topic. In general, the applicable Web sites contained limited but accurate procedural details and offered an interactive forum, most commonly email responses. Photographic documentation was given in less than half the sites reviewed, and most of the results shown were only "good" outcomes. Most sites did not discuss any complications of surgical procedures, but those that did were usually accurate. Eighty-three percent of the sites were biased toward a particular surgical technique. The reviewers believe that only about 15 percent of the sites were acceptable to recommend to their patients. The senior author accessed 17 Web sites that are considered authoritative health information Web sites. Each of these sites was searched for information on breast augmentation by means of its internal search engine. Only 29 percent (5 of 17) had any information in their top 10 hits. Three sites had only chat transcripts. One site had limited but accurate information with a link to the American Society of Plastic Surgeons, and one site had scientific information on product safety. No site met the criteria of accurate, complete information on the surgical procedure of breast augmentation. This study demonstrates that it is difficult for the average layperson to get authoritative information quickly and easily on at least one aspect of cosmetic surgery.

Female↗
PubMed1999

A web-based approach for electrocardiogram monitoring in the home.

A Web-based electrocardiogram (ECG) monitoring service in which a longitudinal clinical record is used for management of patients, is described. The Web application is used to collect clinical data from the patient's home. A database on the server acts as a central repository where this clinical information is stored. A Web browser provides access to the patient's records and ECG data. We discuss the technologies used to automate the retrieval and storage of clinical data from a patient database, and the recording and reviewing of clinical measurement data. On the client's Web browser, ActiveX controls embedded in the Web pages provide a link between the various components including the Web server, Web page, the specialised client side ECG review and acquisition software, and the local file system. The ActiveX controls also implement FTP functions to retrieve and submit clinical data to and from the server. An intelligent software agent on the server is activated whenever new ECG data is sent from the home. The agent compares historical data with newly acquired data. Using this method, an optimum patient care strategy can be evaluated, a summarised report along with reminders and suggestions for action is sent to the doctor and patient by email.

Data Collection↗
PubMed2006

cPath: open source software for collecting, storing, and querying biological pathways.

BACKGROUND: Biological pathways, including metabolic pathways, protein interaction networks, signal transduction pathways, and gene regulatory networks, are currently represented in over 220 diverse databases. These data are crucial for the study of specific biological processes, including human diseases. Standard exchange formats for pathway information, such as BioPAX, CellML, SBML and PSI-MI, enable convenient collection of this data for biological research, but mechanisms for common storage and communication are required. RESULTS: We have developed cPath, an open source database and web application for collecting, storing, and querying biological pathway data. cPath makes it easy to aggregate custom pathway data sets available in standard exchange formats from multiple databases, present pathway data to biologists via a customizable web interface, and export pathway data via a web service to third-party software, such as Cytoscape, for visualization and analysis. cPath is software only, and does not include new pathway information. Key features include: a built-in identifier mapping service for linking identical interactors and linking to external resources; built-in support for PSI-MI and BioPAX standard pathway exchange formats; a web service interface for searching and retrieving pathway data sets; and thorough documentation. The cPath software is freely available under the LGPL open source license for academic and commercial use. CONCLUSION: cPath is a robust, scalable, modular, professional-grade software platform for collecting, storing, and querying biological pathways. It can serve as the core data handling component in information systems for pathway visualization, analysis and modeling.

Computational Biology↗
PubMed2006

DADOS-Survey: an open-source application for CHERRIES-compliant Web surveys.

BACKGROUND: The Internet has been increasingly utilized in biomedical research. From online searching for literature to data sharing, the Internet has emerged as a primary means of research for many physicians and scientists. As a result, Web-based surveys have been employed as an alternative to traditional, paper-based surveys. We describe DADOS-Survey, an open-source Web-survey application developed at our institution that, to the best of our knowledge, is the first to be compliant with the Checklist for Reporting Results of Internet E-Surveys (CHERRIES). DADOS-Survey was designed with usability as a priority, allowing investigators to design and execute their own studies with minimal technical difficulties in doing so. RESULTS: To date, DADOS-Survey has been successfully implemented in five Institutional Review Board-approved studies conducted by various departments within our academic center. Each of these studies employed a Web-survey design as their primary methodology. Our initial experience indicates that DADOS-Survey has been used with relative ease by each of the investigators and survey recipients. This has been further demonstrated through formal and field usability testing, during which time suggestions for improvement were incorporated into the software design. CONCLUSION: DADOS-Survey has the potential to have an important role in the future direction of Web-survey administration in biomedical research. This CHERRIES-compliant application is tailored to the emerging requirements of quality data collection in medicine.

Academic Medical Centers↗
PubMed2003

PedNavigator: a pedigree drawing servlet for large and inbred populations.

PedNavigator is a pedigree drawing application for large and complex pedigrees. It has been developed especially for genetic and epidemiological studies of isolated populations characterized by high inbreeding and multiple matrimonies. PedNavigator is written in Java and is intended as a server-side web application, allowing researchers to 'walk' through family ties by point-and-clicking on person's symbols. The application is able to enrich the pedigree drawings with genotypic and phenotypic information taken from the underlying relational database.

Algorithms↗
PubMed2000

Managing the primary care practice on the Web

Physicians and administrators have little hope of responding appropriately to the challenges of the health care market without data to support decision making. Desired Mayo Clinic s Primary Care Practice was to have the ability to access and integrate data from many platforms in many formats from the Enterprise and bring this information to the desktop in a robust interactive display. The solution was delivery of the data to the Web through an interface using Java with access to Online Analytical Processing (OLAP) tools for summarization, graphical display and reporting. Communicating major trends, assisting in planning and management, visually displaying alerts in summary data and individual patients that are all possible through an easy-to-use Web application. To really understand what the summarized data represents, the physicians must be able to drill down, download and explore their own detail data. A pilot project was developed to test the capabilities of the development environment, the acceptance Web tools, the ability to deliver timely information and the methodology of using a multi-dimensional database to define the data. The Family Medicine practice at four separate locations was chosen for the demonstration project. Two practices in Rochester, MN and practices in two smaller towns, totaling 50 physicians and administrative personnel, were the first clients using the system. A cross-functional team examined a variety of development issues such as data sources, data definitions, levels of security, data analysis types, and style of display. Demonstrations of the prototype met with an overwhelming positive response from administrators and department leaders. The Physician Patient Management solution collects, analyzes, and communicates the information needed to meet today s health care challenges.

Journal Article↗
PubMed2006

Non-invasive light-weight integration engine for building EHR from autonomous distributed systems.

Pangea-LE is a message oriented light-weight integration engine, allowing concurrent access to clinical information from disperse and heterogeneous data sources. The engine extracts the information and serves it to the requester client applications in a flexible XML format. This XML response message can be formatted on demand by the appropriate XSL (Extensible Stylesheet Language) transformation in order to fit client application needs. In this article we present a real use case sample where Pangea-LE collects and generates "on the fly" a structured view of all the patient clinical information available in a healthcare organisation. This information is presented to healthcare professionals in an EHR (Electronic Health Record) viewer Web application with patient search and EHR browsing capabilities. Implantation in a real environment has been a notable success due to the non-invasive method which extremely respects the existing information systems.

Access to Information↗
PubMed2006

caGrid: design and implementation of the core architecture of the cancer biomedical informatics grid.

MOTIVATION: The complexity of cancer is prompting researchers to find new ways to synthesize information from diverse data sources and to carry out coordinated research efforts that span multiple institutions. There is a need for standard applications, common data models, and software infrastructure to enable more efficient access to and sharing of distributed computational resources in cancer research. To address this need the National Cancer Institute (NCI) has initiated a national-scale effort, called the cancer Biomedical Informatics Grid (caBIGtrade mark), to develop a federation of interoperable research information systems. RESULTS: At the heart of the caBIG approach to federated interoperability effort is a Grid middleware infrastructure, called caGrid. In this paper we describe the caGrid framework and its current implementation, caGrid version 0.5. caGrid is a model-driven and service-oriented architecture that synthesizes and extends a number of technologies to provide a standardized framework for the advertising, discovery, and invocation of data and analytical resources. We expect caGrid to greatly facilitate the launch and ongoing management of coordinated cancer research studies involving multiple institutions, to provide the ability to manage and securely share information and analytic resources, and to spur a new generation of research applications that empower researchers to take a more integrative, trans-domain approach to data mining and analysis. AVAILABILITY: The caGrid version 0.5 release can be downloaded from https://cabig.nci.nih.gov/workspaces/Architecture/caGrid/. The operational test bed Grid can be accessed through the client included in the release, or through the caGrid-browser web application http://cagrid-browser.nci.nih.gov.

Biomarkers, Tumor↗
PubMedDate not supplied

Improving knowledge navigation with adaptive hypermedia.

Web applications provide access to a tremendous amount of information: hypertext, hypermedia and on-line databases. However, since users' knowledge, motivation and goals are different, they cannot find the relevant information in the data being diffused. Giving the users applications or environments that will take their differences into account is one way of improving their access to knowledge. The authors' objective is to improve knowledge navigation by adapting users' navigation. Adaptive hypermedia is one way of returning information adapted to the user. This paper presents an adaptive hypermedia system based on user representation with the stereotype model. Both adaptive presentation and navigation techniques are also implemented. This paper focuses on the architecture of the general adaptive hypermedia system as well as adaptivity management. A-TOP, a medical adaptive hypermedia prototype implemented in a hospital intranet system, is described. Adaptive hypermedia is a preliminary approach to the vast problem of user access to knowledge. In conclusion, we hope to extend our reflections to the problems involved in access to knowledge on the World Wide Web (Web).

Computer Graphics↗