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PubMedDate not supplied

A compilation of chiropractic and complementary/alternative medicine (CAM) data from public-use national surveys: report on a health-services research resource for the chiropractic and CAM scientific community.

BACKGROUND: Federally funded national surveys are routinely conducted to provide reliable, valid, and relevant data on health and health care, and these "public-use" survey data are typically made available for further study by the wider scientific community. The full potential for using such data to examine the delivery, utilization, organization, and costs of chiropractic or complementary/alternative (CAM) health care remains largely untapped. OBJECTIVE: To report on a project that identifies and indexes public-use survey databases that contain explicit reference to chiropractic and CAM health care, and compiles that information into a web-based resource for the scientific community. METHODS: Review of database source collections. RESULTS: The utility and efficiency of secondary analyses as a cost-effective research strategy are well appreciated within the larger health-services research community, creating many possible opportunities for productive cooperative research endeavors across scientific disciplines. CONCLUSION: The Chiropractic and Complementary/Alternative Compilation User's Manual is available for free download at http://w3.palmer.edu/carber/manualhome.asp, or by following the links at the Palmer Center for Chiropractic Research homepage.

Chiropractic↗
PubMed2002

MDB: the Metalloprotein Database and Browser at The Scripps Research Institute.

The Metalloprotein Database and Browser (MDB; http://metallo.scripps.edu) at The Scripps Research Institute is a web-accessible resource for metalloprotein research. It offers the scientific community quantitative information on geometrical parameters of metal-binding sites in protein structures available from the Protein Data Bank (PDB). The MDB also offers analytical tools for the examination of trends or patterns in the indexed metal-binding sites. A user can perform interactive searches, metal-site structure visualization (via a Java applet), and analysis of the quantitative data by accessing the MDB through a web browser without requiring an external application or platform-dependent plugin. The MDB also has a non-interactive interface with which other web sites and network-aware applications can seamlessly incorporate data or statistical analysis results from metal-binding sites. The information contained in the MDB is periodically updated with automated algorithms that find and index metal sites from new protein structures released by the PDB.

Algorithms↗
PubMed2006

Babel's tower revisited: a universal resource for cross-referencing across annotation databases.

MOTIVATION: Annotation databases are widely used as public repositories of biological knowledge. However, most of these resources have been developed by independent groups which used different designs and different identifiers for the same biological entities. As we show in this article, incoherent name spaces between various databases represent a serious impediment to using the existing annotations at their full potential. Navigating between various such name spaces by mapping IDs from one database to another is a very important issue which is not properly addressed at the moment. RESULTS: We have developed a web-based resource, Onto-Translate (OT), which effectively addresses this problem. OT is able to map onto each other different types of biological entities from the following annotation databases: Swiss-Prot, TrEMBL, NREF, PIR, Gene Ontology, KEGG, Entrez Gene, GenBank, GenPept, IMAGE, RefSeq, UniGene, OMIM, PDB, Eukaryotic Promoter Database, HUGO Gene Nomenclature Committee and NetAffx. Currently, OT is able to perform 462 types of mappings between 29 different types of IDs from 17 databases concerning 53 organisms. Among these, over 300 types of translations and 15 types of IDs are not currently supported by any other tool or resource. On average, OT is able to correctly map between 96 and 99% of the biological entities provided as input. In terms of speed, sets of approximately 20 000 IDs can be translated in <30 s, in most cases. AVAILABILITY: OT is a part of Onto-Tools, which is freely available at http://vortex.cs.wayne.edu/Projects.html

Database Management Systems↗
PubMed2002

Improving structure-linked access to publicly available chemical toxicity information.

Publicly available toxicity databases serve as the central resource in efforts to develop algorithms for assessing potential chemical toxicity. File standardization and linkage of chemical structures with chemical toxicity information are essential first steps in providing broad access to existing toxicity information, for deriving useful structure-activity relationship (SAR) models, performing analog searches, and estimating the potential toxicity of new chemicals. This review will focus on current efforts to improve structure-linked access to publicly available sources of toxicity information, outlining current web-based resources as well as two new database initiatives for standardizing and consolidating public chemical toxicity information.

Computer Communication Networks↗
PubMed2004

A search tool for identification and analysis of conserved sequence patterns in Saccharomyces spp. orthologous promoter.

We describe a web-based resource to identify, search and analyze sequence patterns conserved in the multiple sequence alignments of orthologous promoters from closely related / distant Saccharomyces spp. The webtool interfaces with a database where conserved sequence patterns (greater than 4 bp) have been previously extracted from genome-wide promoter alignments, allowing one to carry out user-defined genome-wide searches for conserved sequences to assist in the discovery of novel promoter elements based on comparative genomics. The web-based server can be accessed at http://www2.imtech.res.in/ anand/sacch_prom_pat.html.

Base Sequence↗
PubMed2001

STEP--a System for Teaching Experimental Psychology using E-Prime.

Students in psychology need to learn to design and analyze their own experiments. However, software that allows students to build experiments on their own has been limited in a variety of ways. The shipping of the first full release of the E-Prime system later this year will open up a new opportunity for addressing this problem. Because E-Prime promises to become the standard for building experiments in psychology, it is now possible to construct a Web-based resource that uses E-Prime as the delivery engine for a wide variety of instructional materials. This new system, funded by the National Science Foundation, is called STEP (System for the Teaching of Experimental Psychology). The goal of the STEP Project is to provide instructional materials that will facilitate the use of E-Prime in various learning contexts. We are now compiling a large set of classic experiments implemented in E-Prime and available over the Internet from http://step.psy.cmu.edu. The Web site also distributes instructional materials for building courses in experimental psychology based on E-Prime.

Humans↗
PubMed2005

The gene trap resource: a treasure trove for hemopoiesis research.

The laboratory mouse is an invaluable tool for functional gene discovery because of its genetic malleability and a biological similarity to human systems that facilitates identification of human models of disease. A number of mutagenic technologies are being used to elucidate gene function in the mouse. Gene trapping is an insertional mutagenesis strategy that is being undertaken by multiple research groups, both academic and private, in an effort to introduce mutations across the mouse genome. Large-scale, publicly funded gene trap programs have been initiated in several countries with the International Gene Trap Consortium coordinating certain efforts and resources. We outline the methodology of mammalian gene trapping and how it can be used to identify genes expressed in both primitive and definitive blood cells and to discover hemopoietic regulator genes. Mouse mutants with hematopoietic phenotypes derived using gene trapping are described. The efforts of the large-scale gene trapping consortia have now led to the availability of libraries of mutagenized ES cell clones. The identity of the trapped locus in each of these clones can be identified by sequence-based searching via the world wide web. This resource provides an extraordinary tool for all researchers wishing to use mouse genetics to understand gene function.

Animals↗
PubMed2005

Bioinformatics in drug development and assessment.

Bioinformatics is playing an increasingly important role in nearly all aspects of drug discovery, drug assessment, and drug development. This growing importance lies not only in the role that bioinformatics plays in handling large volumes of data, but also in the utility of bioinformatics tools to predict, analyze, or help interpret clinical and preclinical findings. This review focuses on describing and evaluating some of the newer or more important bioinformatics resources (i.e., databases and software) that are of growing importance to understanding or predicting drug metabolism, especially with respect to the absorption, distribution, metabolism, excretion, (ADME), and toxicity (T) of both existing drugs and potential drug leads. Detailed descriptions and critical assessments of a number of potentially useful bioinformatics/cheminformatics databases and predictive ADMET software tools are provided. Additionally, several pharmaceutically important applications of both the databases and software are highlighted. Given the rapid growth in this area and the rapid changes that are taking place, a special emphasis is placed on freely available or Web-accessible resources.

Animals↗
PubMed2003

Working more productively: tools for administrative data.

OBJECTIVE: This paper describes a web-based resource (http://www.umanitoba.ca/centres/mchp/concept/) that contains a series of tools for working with administrative data. This work in knowledge management represents an effort to document, find, and transfer concepts and techniques, both within the local research group and to a more broadly defined user community. Concepts and associated computer programs are made as "modular" as possible to facilitate easy transfer from one project to another. STUDY SETTING/DATA SOURCES: Tools to work with a registry, longitudinal administrative data, and special files (survey and clinical) from the Province of Manitoba, Canada in the 1990-2003 period. DATA COLLECTION: Literature review and analyses of web site utilization were used to generate the findings. PRINCIPAL FINDINGS: The Internet-based Concept Dictionary and SAS macros developed in Manitoba are being used in a growing number of research centers. Nearly 32,000 hits from more than 10,200 hosts in a recent month demonstrate broad interest in the Concept Dictionary. CONCLUSIONS: The tools, taken together, make up a knowledge repository and research production system that aid local work and have great potential internationally. Modular software provides considerable efficiency. The merging of documentation and researcher-to-researcher dissemination keeps costs manageable.

Databases as Topic↗
PubMed2004

FATCAT: a web server for flexible structure comparison and structure similarity searching.

Protein structure comparison, an important problem in structural biology, has two main applications: (i) comparing two protein structures in order to identify the similarities and differences between them, and (ii) searching for structures similar to a query structure. Many web-based resources for both applications are available, but all are based on rigid structural alignment algorithms. FATCAT server implements the recently developed flexible protein structure comparison algorithm FATCAT, which automatically identifies hinges and internal rearrangements in two protein structures. The server provides access to two algorithms: FATCAT-pairwise for pairwise flexible structure comparison and FATCAT-search for database searching for structurally similar proteins. Given two protein structures [in the Protein Data Bank (PDB) format], FATCAT-pairwise reports their structural alignment and the corresponding statistical significance of the similarity measured as a P-value. Users can view the superposition of the structures online in web browsers that support the Chime plug-in, or download the superimposed structures in PDB format. In FATCAT-search, users provide one query structure and the server returns a list of protein structures that are similar to the query, ordered by the P-values. In addition, FATCAT server can report the conformational changes of the query structure as compared to other proteins in the structure database. FATCAT server is available at http://fatcat.burnham.org.

Algorithms↗
PubMed2003

Chlamydomonas reinhardtii genome project. A guide to the generation and use of the cDNA information.

The National Science Foundation-funded Chlamydomonas reinhardtii genome project involves (a) construction and sequencing of cDNAs isolated from cells exposed to various environmental conditions, (b) construction of a high-density cDNA microarray, (c) generation of genomic contigs that are nucleated around specific physical and genetic markers, (d) generation of a complete chloroplast genome sequence and analyses of chloroplast gene expression, and (e) the creation of a Web-based resource that allows for easy access of the information in a format that can be readily queried. Phases of the project performed by the groups at the Carnegie Institution and Duke University involve the generation of normalized cDNA libraries, sequencing of cDNAs, analysis and assembly of these sequences to generate contigs and a set of predicted unique genes, and the use of this information to construct a high-density DNA microarray. In this paper, we discuss techniques involved in obtaining cDNA end-sequence information and the ways in which this information is assembled and analyzed. Descriptions of protocols for preparing cDNA libraries, assembling cDNA sequences and annotating the sequence information are provided (the reader is directed to Web sites for more detailed descriptions of these methods). We also discuss preliminary results in which the different cDNA libraries are used to identify genes that are potentially differentially expressed.

Animals↗
PubMedDate not supplied

Oligonucleotide frequency matrices addressed to recognizing functional DNA sites.

MOTIVATION: Recognition of functional sites remains a key event in the course of genomic DNA annotation. It is well known that a number of sites have their own specific oligonucleotide content. This pinpoints the fact that the preference of the site-specific nucleotide combinations at adjacent positions within an analyzed functional site could be informative for this site recognition. Hence, Web-available resources describing the site-specific oligonucleotide content of the functional DNA sites and applying the above approach for site recognition are needed. However, they have been poorly developed up to now. RESULTS: To describe the specific oligonucleotide content of the functional DNA sites, we introduce the oligonucleotide alphabets, out of which the frequency matrix for a given site could be constructed in addition to a traditional nucleotide frequency matrix. Thus, site recognition accuracy increases. This approach was implemented in the activated MATRIX database accumulating oligonucleotide frequency matrices of the functional DNA sites. We have demonstrated that the false-positive error of the functional site recognition decreases if the oligonucleotide frequency matrixes are added to the nucleotide frequency matrixes commonly used. AVAILABILITY: The MATRIX database is available on the Web, http://wwwmgs.bionet.nsc.ru/Dbases/MATRIX/ and the mirror site, http://www.cbil.upenn.edu/mgs/systems/c onsfreq/.

Algorithms↗
PubMed2006

BioMoby extensions to the Taverna workflow management and enactment software.

BACKGROUND: As biology becomes an increasingly computational science, it is critical that we develop software tools that support not only bioinformaticians, but also bench biologists in their exploration of the vast and complex data-sets that continue to build from international genomic, proteomic, and systems-biology projects. The BioMoby interoperability system was created with the goal of facilitating the movement of data from one Web-based resource to another to fulfill the requirements of non-expert bioinformaticians. In parallel with the development of BioMoby, the European myGrid project was designing Taverna, a bioinformatics workflow design and enactment tool. Here we describe the marriage of these two projects in the form of a Taverna plug-in that provides access to many of BioMoby's features through the Taverna interface. RESULTS: The exposed BioMoby functionality aids in the design of "sensible" BioMoby workflows, aids in pipelining BioMoby and non-BioMoby-based resources, and ensures that end-users need only a minimal understanding of both BioMoby, and the Taverna interface itself. Users are guided through the construction of syntactically and semantically correct workflows through plug-in calls to the Moby Central registry. Moby Central provides a menu of only those BioMoby services capable of operating on the data-type(s) that exist at any given position in the workflow. Moreover, the plug-in automatically and correctly connects a selected service into the workflow such that users are not required to understand the nature of the inputs or outputs for any service, leaving them to focus on the biological meaning of the workflow they are constructing, rather than the technical details of how the services will interoperate. CONCLUSION: With the availability of the BioMoby plug-in to Taverna, we believe that BioMoby-based Web Services are now significantly more useful and accessible to bench scientists than are more traditional Web Services.

Biology↗
PubMed2005

Virtual laboratory manual for microscopic anatomy.

Using digital technology, we have assembled a virtual laboratory manual (VLM) that is a Web-based copy of our traditional laboratory manual. The VLM is used to enhance traditional laboratory instruction in histology. For each reference in the VLM to either a histological slide or an electron micrograph (EM), hyperlinks are included that download digital images derived from the students' glass slide sets or scanned EMs. The VLM serves as an atlas of digital images for concurrent study of similar sections by light microscopy during laboratory sessions. In addition, students can review the images from the VLM at remote locations. We have encouraged continued use of light microscopes in laboratories by basing the majority of practical examination identifications on analysis of marked histological slides that require students to use their own microscopes. The VLM provides the convenience of a Web-based resource with high-quality images, yet allows retention of the many excellent traditional aspects of our course. An example of a VLM laboratory on epithelium is available online (http://users.von.uc.edu/michaeje/VLM-Epithelium/exLab4.pdf).

Computer-Assisted Instruction↗
PubMed1996

Cystic fibrosis resources on the World Wide Web.

A great deal of information is currently available on the Internet concerning the complex and life-threatening genetic disorder cystic fibrosis (CF). The disease is caused by mutations in the gene encoding the cystic fibrosis transmembrane conductance regulator (CFTR). World Wide Web (WWW) sites offer a range of information from gene structure and function to individual discussion groups. Specifically, they allow access to CFTR nucleic predicted protein sequences, pages for medical doctors and researchers, and support-group sites directed towards CF patients, their families and friends.

Computer Communication Networks↗
PubMed2005

DICOM demystified: a review of digital file formats and their use in radiological practice.

Digital imaging and communications in medicine (DICOM) is the standard image file format used by radiological hardware devices. This article will provide an overview of DICOM and attempt to demystify the bewildering number of image formats that are commonly encountered. The characteristics and usefulness of different image file types will be explored and a variety of freely available web-based resources to aid viewing and manipulation of digital images will be reviewed. How best to harness DICOM technology before the introduction of picture archiving and communication systems (PACS) will also be described.

Humans↗
PubMed2004

Toward consistent assignment of structural domains in proteins.

The assignment of protein domains from three-dimensional structure is critically important in understanding protein evolution and function, yet little quality assurance has been performed. Here, the differences in the assignment of structural domains are evaluated using six common assignment methods. Three human expert methods (AUTHORS (authors' annotation), CATH and SCOP) and three fully automated methods (DALI, DomainParser and PDP) are investigated by analysis of individual methods against the author's assignment as well as analysis based on the consensus among groups of methods (only expert, only automatic, combined). The results demonstrate that caution is recommended in using current domain assignments, and indicates where additional work is needed. Specifically, the major factors responsible for conflicting domain assignments between methods, both experts and automatic, are: (1) the definition of very small domains; (2) splitting secondary structures between domains; (3) the size and number of discontinuous domains; (4) closely packed or convoluted domain-domain interfaces; (5) structures with large and complex architectures; and (6) the level of significance placed upon structural, functional and evolutionary concepts in considering structural domain definitions. A web-based resource that focuses on the results of benchmarking and the analysis of domain assignments is available at

Algorithms↗