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PubMed2006

The University of Washington Health Sciences Library BioCommons: an evolving Northwest biomedical research information support infrastructure.

SETTING: The University of Washington Health Sciences Libraries and Information Center BioCommons serves the bioinformatics needs of researchers at the university and in the vibrant for-profit and not-for-profit biomedical research sector in the Washington area and region. PROGRAM COMPONENTS: The BioCommons comprises services addressing internal University of Washington, not-for-profit, for-profit, and regional and global clientele. The BioCommons is maintained and administered by the BioResearcher Liaison Team. The BioCommons architecture provides a highly flexible structure for adapting to rapidly changing resources and needs. EVALUATION MECHANISMS: BioCommons uses Web-based pre- and post-course evaluations and periodic user surveys to assess service effectiveness. Recent surveys indicate substantial usage of BioCommons services and a high level of effectiveness and user satisfaction. NEXT STEPS/FUTURE DIRECTIONS: BioCommons is developing novel collaborative Web resources to distribute bioinformatics tools and is experimenting with Web-based competency training in bioinformation resource use.

Academic Medical Centers↗

PubMed2006

Heuristic evaluation of a Web-based Educational Resource for low literacy NICU parents.

"Web-based Educational Resources for the NICU Parent," an educational website for low literacy families, was developed and implemented as prototype web pages using Macromedia Dreamweaver MX. Research has shown that evaluating a website before its implementation can reduce usability errors and improve the overall interface design. As an initial assessment of the website's interface, a heuristic evaluation was conducted with a sample of three usability experts. The usability experts reviewed the website with typical case scenario and completed an evaluation form covering ten usability heuristics. The task was completed in approximately one and a half hours; 82 heuristic violations were reported. The heuristic violations noted on the evaluation forms and the experts' verbalizations captured by a usability testing tool (Morae) were content analyzed and categorized based on the potential design solutions to be implemented: function, design and layout, content, and navigation. Approximately 88% of the violations were resolved by implementing these solutions. The study findings suggest that the heuristic evaluation was an efficient and inexpensive method for evaluating the low literacy interface of the "Web-based Educational Resources for the NICU Parent."

Comprehension↗

PubMed2003

Generic design of Web-based clinical databases.

BACKGROUND: The complexity and the rapid evolution and expansion of the domain of clinical information make development and maintenance of clinical databases difficult. Whenever new data types are introduced or existing types are modified in a conventional relational database system, the physical design of the database must be changed accordingly. For this reason, it is desirable that a clinical database be flexible and allow for modifications and for addition of new types of data without having to change the physical database schema. The ideal clinical database would therefore implement a highly-detailed logical database schema in a completely-generic physical schema that stores the wide variety of clinical data in a small and constant number of tables. OBJECTIVE: The objective was to review the medical literature regarding generic design of clinical databases. METHODS: A search strategy was devised for PubMed and Google to get the best match of peer-reviewed articles and free Web resources on the subject. RESULTS: Eight peer reviewed articles and a Web tutorial were found. All the resources described the so-called Entity-Attribute-Value (EAV) design as a means of simplifying the physical layout of data tables in a clinical database. In Entity-Attribute-Value design all data can be stored in a single generic table with conceptually 3 columns: 1 for entity (eg, patient identification), 1 for attribute (eg, name), and 1 for value (eg, "Jens Hansen"). To add more descriptive fields to the entity class, all that is necessary is to add attribute values to be stored in the attribute field. The main advantages of the Entity-Attribute-Value design are flexibility and effective entity-centered data retrieval. The main disadvantages are complicated front-end programming needed to display data in a conventional layout that the user understands and less-efficient attribute-centered queries. The Internet offers unique opportunities for database deployment, eliminating problems of user-interface deployment. Furthermore, Web forms may be generated in a completely-generic fashion during run time from metadata describing the semantic structure of clinical information stored in the database. CONCLUSIONS: The Entity-Attribute-Value model is useful for generic design of clinical databases. Depending on the specific requirements of the application, more or less complex metadata models may be applied.

Databases, Factual↗

PubMed1997

Linking a clinical system to heterogeneous information resources.

We present a model for providing clinical information system (CIS) users with quick access to high quality information resources. We have developed a chest X-ray information button application which is attached to the chest X-ray reports in the CIS at the Columbia Presbyterian Medical Center. The application generates questions based on clinical information, user interest, generic question templates, and resource availability. It then provides answers to the questions through integrated access to heterogeneous information resources including the CIS itself and publicly accessible Web resources.

Computer Communication Networks↗

PubMed2000

Mouse-human comparative map resources on the Web.

Comparative maps have been a valuable resource for extrapolating biological information among organisms. The relationship between mouse and human maps provides a framework for integrating information from each species and thereby increasing the utility of all available data such as gene location, structure and function. This review describes the various public resources, both databases and web sites, containing genome-wide mouse-human comparative map information available through the World-Wide Web. We will focus on the use and applicability of these resources in their current form and consider future potential directions.

Animals↗

PubMed2005

Indexing method of digital audiovisual medical resources with semantic Web integration.

Digitalization of audiovisual resources and network capability offer many possibilities which are the subject of intensive work in scientific and industrial sectors. Indexing such resources is a major challenge. Recently, the Motion Pictures Expert Group (MPEG) has developed MPEG-7, a standard for describing multimedia content. The goal of this standard is to develop a rich set of standardized tools to enable efficient retrieval from digital archives or the filtering of audiovisual broadcasts on the Internet. How could this kind of technology be used in the medical context? In this paper, we propose a simpler indexing system, based on the Dublin Core standard and compliant to MPEG-7. We use MeSH and the UMLS to introduce conceptual navigation. We also present a video-platform which enables encoding and gives access to audiovisual resources in streaming mode.

Abstracting and Indexing↗

PubMed1996

Building the electronic health sciences library for the twenty-first century: the Galter Library experience.

Constructing home pages for World-Wide Web access has become a major activity in academic health sciences libraries. At the Northwestern University, Galter Health Sciences Library staff are creating the library's new health information system using Web resources and integrating them with existing library systems-NUmed (OVID MEDLINE) and LUIS/NUcat (NOTIS). Development of Web pages, including selection and organization of electronic information, has become the building process for the electronic library. Selection, organization, design, and construction are important factors in the creation of an efficient and useful information system. Using resources like the World-Wide Web and tools like Netscape, library staff are designing an interface, defining policies and guidelines, and creating the tools that will give users easy access to local and international electronic, scholarly information resources. In this paper, the process used at Northwestern is shown as a model of an electronic health sciences library for the twenty-first century.

Academic Medical Centers↗

PubMed2005

The PANTHER database of protein families, subfamilies, functions and pathways.

PANTHER is a large collection of protein families that have been subdivided into functionally related subfamilies, using human expertise. These subfamilies model the divergence of specific functions within protein families, allowing more accurate association with function (ontology terms and pathways), as well as inference of amino acids important for functional specificity. Hidden Markov models (HMMs) are built for each family and subfamily for classifying additional protein sequences. The latest version, 5.0, contains 6683 protein families, divided into 31,705 subfamilies, covering approximately 90% of mammalian protein-coding genes. PANTHER 5.0 includes a number of significant improvements over previous versions, most notably (i) representation of pathways (primarily signaling pathways) and association with subfamilies and individual protein sequences; (ii) an improved methodology for defining the PANTHER families and subfamilies, and for building the HMMs; (iii) resources for scoring sequences against PANTHER HMMs both over the web and locally; and (iv) a number of new web resources to facilitate analysis of large gene lists, including data generated from high-throughput expression experiments. Efforts are underway to add PANTHER to the InterPro suite of databases, and to make PANTHER consistent with the PIRSF database. PANTHER is now publicly available without restriction at http://panther.appliedbiosystems.com.

Animals↗

PubMedDate not supplied

Patient safety and teamwork in perinatal care: resources for clinicians.

Recent data reveal communication issues and organizational culture to be key factors in adverse perinatal outcomes. Hierarchical communication is common in healthcare and can be a significant impediment to safe care. Principles of teamwork employed by other industries, such as aviation and the military, can be appropriately applied to healthcare. This article provides a brief introduction to Crew Resource Management as well as a listing of print, multimedia, and Web resources for clinicians interested in promoting cultural change and effective teamwork.

Communication↗

PubMed2005

Web-based educational resources for low literacy families in the NICU.

Web-based educational resources for families in the neonatal intensive care unit (NICU)with low health literacy were developed and implemented as prototype web pages using Macromedia Dreamweaver MX. The user interface was designed for a touch-screen platform with voice-recorded messages to incorporate parents' varying literacy levels and computer experience. Cognitive load theory was used to guide the organization and presentation of information. The text was translated to a 6th grade reading level by Flesch-Kincaid Grade Level, MS Word.

Comprehension↗

PubMedDate not supplied

Spanish health information resources for nurses.

According to the U.S. Census Bureau, Spanish-speakers currently constitute 1 in 10 U.S. households, and the number is expected to rise. To provide responsible and responsive care, many nurses will need to develop communication skills for working with Spanish speakers and be able to find quality, reliable health information in Spanish for their patients and patients' families. A number of efforts have been described in the literature. This article augments prior efforts by providing nurses with resources for learning key words and phrases, sources to increase awareness of and sensitivity to cultural nuances, reliable consumer Web resources for Spanish-speaking patients, and tips for evaluating Spanish language health information on other Web sites.

Directories as Topic↗

PubMed2004

A web server for performing electronic PCR.

'Electronic PCR' (e-PCR) refers to a computational procedure that is used to search DNA sequences for sequence tagged sites (STSs), each of which is defined by a pair of primer sequences and an expected PCR product size. To gain speed, our implementation extracts short 'words' from the 3' end of each primer and stores them in a sorted hash table that can be accessed efficiently during the search. One recent improvement is the use of overlapping discontinuous words to allow matches to be found despite the presence of a mismatch. Moreover, it is possible to allow gaps in the alignment between the primer and the sequence. The effect of these changes is to improve sensitivity without significantly affecting specificity. The new software provides a search mode using a query STS against a sequence database to augment the previously available mode using a query sequence against an STS database. Finally, e-PCR may now be used through a web service, with search results linked to other web resources such as the UniSTS database and the MapViewer genome browser. The e-PCR web server may be found at www.ncbi.nlm.nih.gov/sutils/e-pcr.

Algorithms↗

PubMed2002

Public health, GIS, and the internet.

Internet access and use of georeferenced public health information for GIS application will be an important and exciting development for the nation's Department of Health and Human Services and other health agencies in this new millennium. Technological progress toward public health geospatial data integration, analysis, and visualization of space-time events using the Web portends eventual robust use of GIS by public health and other sectors of the economy. Increasing Web resources from distributed spatial data portals and global geospatial libraries, and a growing suite of Web integration tools, will provide new opportunities to advance disease surveillance, control, and prevention, and insure public access and community empowerment in public health decision making. Emerging supercomputing, data mining, compression, and transmission technologies will play increasingly critical roles in national emergency, catastrophic planning and response, and risk management. Web-enabled public health GIS will be guided by Federal Geographic Data Committee spatial metadata, OpenGIS Web interoperability, and GML/XML geospatial Web content standards. Public health will become a responsive and integral part of the National Spatial Data Infrastructure.

Geographic Information Systems↗

PubMed2005

Principles of haplotype mapping and potential applications to attention-deficit/hyperactivity disorder.

Approaches to the study of common, complex genetic disorders like attention-deficit/hyperactivity disorder (ADHD) are evolving rapidly. Traditional linkage and association mapping each have distinct roles to play. Rapid advances in genomic information and technologies make association studies more attractive, including the possibility in the near future of whole genome association scans. This review covers the following broad topics: 1) the principles of linkage and association analyses as they apply to ADHD, and 2) the implications of genome architecture for association studies of complex diseases like ADHD. The structure of linkage disequilibrium is approached through review of the statistical measures of allelic associations and their relationship to observed haplotypes. The patterns of haplotypes across the human genome are discussed, as well as the implications of linkage disequilibrium mapping for association studies in general and ADHD specifically. Finally, the extent to which the allelic architecture of a candidate ADHD gene is publicly available and the web resources to access this information are covered. Today, the wealth of polymorphism data available on the worldwide web enables researchers to focus powerful methodologic tools on candidate genes and regions of interest. Coupling this with larger patient collections and more refined phenotyping will move forward the identification of disease-associated polymorphisms and ultimately the development of genetically based pharmaceuticals and diagnostic tests.

Attention Deficit Disorder with Hyperactivity↗

PubMed1998

GeneCards: a novel functional genomics compendium with automated data mining and query reformulation support.

MOTIVATION: Modern biology is shifting from the 'one gene one postdoc' approach to genomic analyses that include the simultaneous monitoring of thousands of genes. The importance of efficient access to concise and integrated biomedical information to support data analysis and decision making is therefore increasing rapidly, in both academic and industrial research. However, knowledge discovery in the widely scattered resources relevant for biomedical research is often a cumbersome and non-trivial task, one that requires a significant amount of training and effort. RESULTS: To develop a model for a new type of topic-specific overview resource that provides efficient access to distributed information, we designed a database called 'GeneCards'. It is a freely accessible Web resource that offers one hypertext 'card' for each of the more than 7000 human genes that currently have an approved gene symbol published by the HUGO/GDB nomenclature committee. The presented information aims at giving immediate insight into current knowledge about the respective gene, including a focus on its functions in health and disease. It is compiled by Perl scripts that automatically extract relevant information from several databases, including SWISS-PROT, OMIM, Genatlas and GDB. Analyses of the interactions of users with the Web interface of GeneCards triggered development of easy-to-scan displays optimized for human browsing. Also, we developed algorithms that offer 'ready-to-click' query reformulation support, to facilitate information retrieval and exploration. Many of the long-term users turn to GeneCards to quickly access information about the function of very large sets of genes, for example in the realm of large-scale expression studies using 'DNA chip' technology or two-dimensional protein electrophoresis. AVAILABILITY: Freely available at http://bioinformatics.weizmann.ac.il/cards/ CONTACT: cards@bioinformatics.weizmann.ac.il

Algorithms↗

PubMed2001

The RESID Database of protein structure modifications and the NRL-3D Sequence-Structure Database.

The RESID Database is a comprehensive collection of annotations and structures for protein post-translational modifications including N-terminal, C-terminal and peptide chain cross-link modifications. The RESID Database includes systematic and frequently observed alternate names, Chemical Abstracts Service registry numbers, atomic formulas and weights, enzyme activities, taxonomic range, keywords, literature citations with database cross-references, structural diagrams and molecular models. The NRL-3D Sequence-Structure Database is derived from the three-dimensional structure of proteins deposited with the Research Collaboratory for Structural Bioinformatics Protein Data Bank. The NRL-3D Database includes standardized and frequently observed alternate names, sources, keywords, literature citations, experimental conditions and searchable sequences from model coordinates. These databases are freely accessible through the National Cancer Institute-Frederick Advanced Biomedical Computing Center at these web sites: http://www. ncifcrf.gov/RESID, http://www.ncifcrf.gov/NRL-3D; or at these National Biomedical Research Foundation Protein Information Resource web sites: http://pir.georgetown.edu/pirwww/dbinfo/resid .html, http://pir.georgetown.edu/pirwww/dbinfo/nrl3d .html

Amino Acids↗

PubMed2002

Communication issues in migraine diagnosis.

OBJECTIVES: To examine the importance of good communication when informing the patient of the diagnosis of migraine; to review the essentials of successful communication between physician and patient on the aspect of diagnosis; to survey learning resources for physicians on communicating information to patients. METHODS: This paper is based on observations made by the author of the successful interactions of numerous international "headache experts" with their patients, on a review of the medical education literature pertaining to the teaching of communication skills, and on 30 years of not always successful communication with patients. RESULTS: Communicating the diagnosis of migraine is an opportunity to educate and reassure the patient, to lay the foundation for rational treatment and to help establish the successful doctor-patient relationship which is essential for effective management. No matter how accurate the diagnosis, failure to communicate it effectively to the patient (and often to significant others) may impair interactions with the patient and compromise therapy. Effective communication of a diagnosis requires clarity, relevance to the patient, a positive attitude, and reinforcement through repetition, questioning and dialogue. In terms of using the diagnosis to lay a foundation for therapy, it is useful to explain the symptoms as transient physical dysfunction of normal tissues, to indicate that there are multiple mechanisms underlying the dysfunction of which only some may presently be susceptible to treatment and to stress the relevance of emotions as factors which may powerfully affect, for better or worse, the underlying disturbed physiology of migraine. Into this model can be "plugged" all the relevant therapies for migraine. This is the ideal, but every day experience in the headache consultant's office suggest that in both primary care and specialist practice, it is infrequently attained. There are scant resources other than example for physicians to learn communication of headache diagnosis specifically but there are numerous print and web resources available to physicians wh wish to learn and/or teach the generic principles of effective communication, and these principles require little or no modification to be applied to the headache patient and the headache doctor.

Communication↗

PubMed2001

SeWeR: a customizable and integrated dynamic HTML interface to bioinformatics services.

SUMMARY: Sequence analysis using Web Resources (SeWeR) is an integrated, Dynamic HTML (DHTML) interface to commonly used bioinformatics services available on the World Wide Web. It is highly customizable, extendable, platform neutral, completely server-independent and can be hosted as a web page as well as being used as stand-alone software running within a web browser.

Computational Biology↗