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At least 235 records · Page 13Linked to original sources
PubMed2003

Achieving evolvable Web-database bioscience applications using the EAV/CR framework: recent advances.

The EAV/CR framework, designed for database support of rapidly evolving scientific domains, utilizes metadata to facilitate schema maintenance and automatic generation of Web-enabled browsing interfaces to the data. EAV/CR is used in SenseLab, a neuroscience database that is part of the national Human Brain Project. This report describes various enhancements to the framework. These include (1) the ability to create "portals" that present different subsets of the schema to users with a particular research focus, (2) a generic XML-based protocol to assist data extraction and population of the database by external agents, (3) a limited form of ad hoc data query, and (4) semantic descriptors for interclass relationships and links to controlled vocabularies such as the UMLS.

Database Management Systems↗
PubMedDate not supplied

Traditional Chinese medicine database and application on the Web.

To study traditional Chinese medicines and exchange related information through the worldwide Web, we developed a traditional Chinese medicine database and a program for searching and displaying data in the database on the Web. In this paper, the traditional Chinese medicine database is briefly introduced; the methods used in developing the program, including ISAPI (Microsoft Internet Server Application Programming Interface), VRML (Virtual Reality Model Language), and JavaScript are described; and three application examples are also given.

Databases, Factual↗
PubMed1999

World Wide Web and Internet: applications for radiologists.

Global exchange of information is one of the major sources of scientific progress in medicine. For management of the rapidly growing body of medical information, computers and their applications have become an indispensable scientific tool. Approximately 36 million computer users are part of a worldwide network called the Internet or "information highway" and have created a new infrastructure to promote rapid and efficient access to medical, and thus also to radiological, information. With the establishment of the World Wide Web (WWW) by a consortium of computer users who used a standardized, nonproprietary syntax termed HyperText Markup Language (HTML) for composing documents, it has become possible to provide interactive multimedia presentations to a wide audience. The extensive use of images in radiology makes education, worldwide consultation (review) and scientific presentation via the Internet a major beneficiary of this technical development. This is possible, since both information (text) as well as medical images can be transported via the Internet. Presently, the Internet offers an extensive database for radiologists. Since many radiologists and physicians have to be considered "Internet novices" and, hence, cannot yet avail themselves of the broad spectrum of the Internet, the aim of this article is to present a general introduction to the WWW/Internet and its applications for radiologists. All Internet sites mentioned in this article can be found at the following Internet address: http://www.univie.ac. at/radio/radio.html (Department of Radiology, University of Vienna)

Humans↗
PubMed2004

PTGL--a web-based database application for protein topologies.

Protein Topology Graph Library (PTGL) is a database application for the representation and retrieval of protein topologies. Protein topologies are based on a graph-theoretical protein model at secondary structure level. Different views on protein topology are given by four linear notations for their characterization. Protein topologies can be derived at different description levels considering alpha- and beta-structures. The on-line search tool is based on an object-relational database and provides a query browser for data interrogation by string patterns, keyword queries and sequence similarity. Protein topologies are represented both as schematic diagrams and as three-dimensional images.

Computer Graphics↗
PubMed2005

Structural semantic interconnections: a knowledge-based approach to word sense disambiguation.

Word Sense Disambiguation (WSD) is traditionally considered an Al-hard problem. A break-through in this field would have a significant impact on many relevant Web-based applications, such as Web information retrieval, improved access to Web services, information extraction, etc. Early approaches to WSD, based on knowledge representation techniques, have been replaced in the past few years by more robust machine learning and statistical techniques. The results of recent comparative evaluations of WSD systems, however, show that these methods have inherent limitations. On the other hand, the increasing availability of large-scale, rich lexical knowledge resources seems to provide new challenges to knowledge-based approaches. In this paper, we present a method, called structural semantic interconnections (SSI), which creates structural specifications of the possible senses for each word in a context and selects the best hypothesis according to a grammar G, describing relations between sense specifications. Sense specifications are created from several available lexical resources that we integrated in part manually, in part with the help of automatic procedures. The SSI algorithm has been applied to different semantic disambiguation problems, like automatic ontology population, disambiguation of sentences in generic texts, disambiguation of words in glossary definitions. Evaluation experiments have been performed on specific knowledge domains (e.g., tourism, computer networks, enterprise interoperability), as well as on standard disambiguation test sets.

Algorithms↗
PubMed2005

ATLes: the strategic application of Web-based technology to address learning objectives and enhance classroom discussion in a veterinary pathology course.

A case-based program called ATLes (Adaptive Teaching and Learning Environments) was designed for use in a systemic pathology course and implemented over a four-year period. Second-year veterinary students working in small collaborative learning groups used the program prior to their weekly pathology laboratory. The goals of ATLes were to better address specific learning objectives in the course (notably the appreciation of pathophysiology), to solve previously identified problems associated with information overload and information sorting that commonly occur as part of discovery-based processes, and to enhance classroom discussion. The program was also designed to model and allow students to practice the problem-oriented approach to clinical cases, thereby enabling them to study pathology in a relevant clinical context. Features included opportunities for students to obtain additional information on the case by requesting specific laboratory tests and/or diagnostic procedures. However, students were also required to justify their diagnostic plans and to provide mechanistic analyses. The use of ATLes met most of these objectives. Student acceptance was high, and students favorably reviewed the online ''Content Links'' that made useful information more readily accessible and level appropriate. Students came to the lab better prepared to engage in an in-depth and high-quality discussion and were better able to connect clinical problems to underlying changes in tissue (lesions). However, many students indicated that the required time on task prior to lab might have been excessive relative to what they thought they learned. The classroom discussion, although improved, was not elevated to the expected level-most likely reflecting other missing elements of the learning environment, including the existing student culture and the students' current discussion skills. This article briefly discusses the lessons learned from ATLes and how similar case-based exercises might be combined with other approaches to enhance and enliven classroom discussions in the veterinary curriculum.

Computer-Assisted Instruction↗
PubMed1996

Just tell me what you want!: the promise and perils of rapid prototyping with the World Wide Web.

Construction of applications using the World Wide Web architecture and Hypertext Markup Language (HTML) documents is relatively simple. We are exploring this approach with an application, called PolyMed now in use by surgical residents for one year. We monitored use and obtained user feedback to develop new features and eliminate undesirable ones. The system has been used to keep track of over 4,200 patients. We predicted, several advantages and disadvantages to this approach to prototyping clinical applications. Our experience confirms some advantages (ease of development and customization, ability to exploit non-Web system components, and simplified user interface design) and disadvantages (lack of database management services). Some predicted disadvantages failed to materialize (difficulty modeling a clinical application with hypertext and inconveniences associated with the "connectionless" nature of the Web). We were disappointed to find that while integration of external Web applications (such as Medline) into our application was easy, our users did not find it useful.

Attitude to Computers↗
PubMed2002

Building an asynchronous web-based tool for machine learning classification.

Various unsupervised and supervised learning methods including support vector machines, classification trees, linear discriminant analysis and nearest neighbor classifiers have been used to classify high-throughput gene expression data. Simpler and more widely accepted statistical tools have not yet been used for this purpose, hence proper comparisons between classification methods have not been conducted. We developed free software that implements logistic regression with stepwise variable selection as a quick and simple method for initial exploration of important genetic markers in disease classification. To implement the algorithm and allow our collaborators in remote locations to evaluate and compare its results against those of other methods, we developed a user-friendly asynchronous web-based application with a minimal amount of programming using free, downloadable software tools. With this program, we show that classification using logistic regression can perform as well as other more sophisticated algorithms, and it has the advantages of being easy to interpret and reproduce. By making the tool freely and easily available, we hope to promote the comparison of classification methods. In addition, we believe our web application can be used as a model for other bioinformatics laboratories that need to develop web-based analysis tools in a short amount of time and on a limited budget.

Algorithms↗
PubMed2005

Aspects of residency programs' web sites important to student applicants.

OBJECTIVES: To determine which components of a residency Web site (RWS) are important to residency applicants. METHODS: The authors performed a cross-sectional observational study of residency applicants. All applicants were invited to participate and were provided with a nine-question survey. Applicants were asked questions regarding the importance and impact of RWSs on the residency application process. They were also asked to rate items regarding content and aesthetics, and then rank all items in order of importance. Descriptive statistics are reported. Rank-order displays were determined using the Condorcet choice method. RESULTS: One hundred eighty-eight (82%) of the applicants responded to the survey. Seventy-eight percent of the respondents reported that information provided in an RWS influenced their decision to apply to a particular program (41% decided not to apply to at least one program based on the quality of its RWS). Applicants believed that presentation of the residency curriculum was most important. Information about the hospital and its affiliates, faculty and resident information, and research activities followed in the rank order. Least important to applicants were the aesthetic quality of the site, faculty/resident photographs, and educational resource materials. The authors report additional areas of content that applicants thought would be useful to view. CONCLUSIONS: The content, and not necessarily the aesthetic quality, of an RWS is important to residency applicants. The residency program Web site would seem to be an important factor in the applicant's decision to apply. The applicant's perspective provides training program directors and administrators with focused direction in Web site development or for upgrading existing RWSs for use by future applicants.

Career Choice↗
PubMed1998

A generic model for Internet-accessed databases in epidemiology: a nutritional application.

The Web technology has made the exchange of information among heterogeneous platforms possible with no added cost to end-users. Adding to this, it made it possible to access databases residing on servers in different geographic locations giving thus conceptors and programmers the possibility of making distributed applications with a fraction of the time needed before. This technology is therefore very well suited to medical applications which are normally multi-user, multiplatform, and data-intensive. In this paper, we present an application for epidemiological studies based on the Web technology and the reuse of common concepts in epidemiology to produce a generic model that can be parameterisable by the end-user to suit the needs of his study. This model is then applied to develop an application to optimise the collection and processing of nutritional data for a nation-wide epidemiological study concerning renal failure patients.

Databases, Factual↗
PubMed2006

pSTIING: a 'systems' approach towards integrating signalling pathways, interaction and transcriptional regulatory networks in inflammation and cancer.

pSTIING (http://pstiing.licr.org) is a new publicly accessible web-based application and knowledgebase featuring 65 228 distinct molecular associations (comprising protein-protein, protein-lipid, protein-small molecule interactions and transcriptional regulatory associations), ligand-receptor-cell type information and signal transduction modules. It has a particular major focus on regulatory networks relevant to chronic inflammation, cell migration and cancer. The web application and interface provide graphical representations of networks allowing users to combine and extend transcriptional regulatory and signalling modules, infer molecular interactions across species and explore networks via protein domains/motifs, gene ontology annotations and human diseases. pSTIING also supports the direct cross-correlation of experimental results with interaction information in the knowledgebase via the CLADIST tool associated with pSTIING, which currently analyses and clusters gene expression, proteomic and phenotypic datasets. This allows the contextual projection of co-expression patterns onto prior network information, facilitating the identification of functional modules in physiologically relevant systems.

Amino Acid Motifs↗
PubMed2004

Java-based application framework for visualization of gene regulatory region annotations.

MOTIVATION: The genome sequences of several organisms are either complete, or being sequenced. Each genome needs to be integrated with various types of annotations, e.g. locations of genes, promoters and other functional elements such as transcriptional regulatory elements. A robust application framework will be useful for developing web-based applications to visualize various genome annotations. RESULTS: We developed genome data visualization toolkit (GDVTK) as an application framework that consists of a set of data structures and core classes, using Java technology. GDVTK is a sound framework for developing web-based applications to present the gene regulatory region annotations in visual form. The current version of GDVTK consists of eight packages and 38 Java classes that are portable, reusable and extensible for plugging in new data sources and models. We implemented GDVTK for visualization of promoter annotations in Mammalian Promoter Database (MPromDb), a web-based gene-regulatory information server. AVAILABILITY: GDVTK is available under GNU general public license. Source code and software documentation can be found at the URL http://bioinformatics.med.ohio-state.edu/GDVTK.

Computer Graphics↗
PubMed2006

Maintaining excellence in physician nurse communication with CPOE: A nursing informatics team approach.

Designing and implementing CPOE systems is difficult, presenting many challenges to overcome related to workflow redesign. As part of the Mayo Clinic Arizona CPOE design and implementation, it was recognized that physicians would be placing inpatient orders from multiple locations; therefore nurses no longer would have the usual visual clues to identify new physician orders. This could easily lead to a delay in implementing orders that require immediate action. To address this, a multidisciplinary team evaluated various communication options and designed two in-house Web-based applications to solve the communication gap. One application will provide staff nurses with visual alerts for stat and routine orders as they are processed in real time. A second application is a Web-based link to the nursing assignment sheets, which will give physicians and support staff access to staff nurse assignments and phone numbers, specific to each nursing unit.

Arizona↗
PubMed2006

Biotool2Web: creating simple Web interfaces for bioinformatics applications.

UNLABELLED: Currently there are many bioinformatics applications being developed, but there is no easy way to publish them on the World Wide Web. We have developed a Perl script, called Biotool2Web, which makes the task of creating web interfaces for simple ('home-made') bioinformatics applications quick and easy. Biotool2Web uses an XML document containing the parameters to run the tool on the Web, and generates the corresponding HTML and common gateway interface (CGI) files ready to be published on a web server. AVAILABILITY: This tool is available for download at URL http://www.uni-muenster.de/Bioinformatics/services/biotool2web/ CONTACT: Georg Fuellen (fuellen@alum.mit.edu).

Computational Biology↗