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PubMed1998

MHCWeb: converting a WWW database into a knowledge-based collaborative environment.

The World Wide Web (WWW) is useful for distributing scientific data. Most existing web data resources organize their information either in structured flat files or relational databases with basic retrieval capabilities. For databases with one or a few simple relations, these approaches are successful, but they can be cumbersome when there is a data model involving multiple relations between complex data. We believe that knowledge-based resources offer a solution in these cases. Knowledge bases have explicit declarations of the concepts in the domain, along with the relations between them. They are usually organized hierarchically, and provide a global data model with a controlled vocabulary. We have created the OWEB architecture for building online scientific data resources using knowledge bases. OWEB provides a shell for structuring data, providing secure and shared access, and creating computational modules for processing and displaying data. In this paper, we describe the translation of the online immunological database MHCPEP into an OWEB system called MHCWeb. This effort involved building a conceptual model for the data, creating a controlled terminology for the legal values for different types of data, and then translating the original data into the new structure. The OWEB environment allows for flexible access to the data by both users and computer programs.

Artificial Intelligence↗
PubMed2005

Ontology driven dynamic linking of biology resources.

Biologists were early adopters of the Web and continue to use it as the primary means of delivering data, tools and knowledge to their community. The Web is made by the links between pages, yet these links have many limitations: they are static and maintained by hand; they can only link one lexical item to another single resource; ownership is necessary for the placement of link anchors and the link mechanism is essentially inflexible. Dynamic linking services, supported by ontologies, offer a mechanism to overcome such restrictions. The Conceptual Open Hypermedia Service (COHSE) system enhances web resources through the dynamic addition of hypertext links. These links are derived through the use of an ontology and associated lexicon along with a mapping from concepts to possible link targets. We describe an application of COHSE to Bioinformatics, using the Gene Ontology (GO) as an ontology and associated keyword mappings and GO associations as link targets. The resulting demonstrator (referred to here as GOHSE) provides both glossary functionality and the possibility of building knowledge based hypertext structures linking bioinformatics resources.

Animals↗
PubMed2004

Child safety education and the world wide web: an evaluation of the content and quality of online resources.

The purpose of this study was to assess the content, quality, and type of internet resources available for safety education. Using 19 search engines with search strings targeting major forms of injury, identified resources were classified by audience group, accessibility, and authorship. Two independent reviewers rated each resource on the basis of its content and a set of quality criteria using a three point scale. Overall, 10 (18.2%) resources were of highest quality, four (7.3%) were intermediate, and 41 (74.5%) were not recommended. Eighteen months after the original search, 67.3% of all resources and 90% of the highest quality resources were still on the internet. This study provides a methodology for evaluating child safety resources on the world wide web and demonstrates that most internet resources for safety education are of dubious quality. A rating system such as the one developed for this study may be used to identify valuable internet materials.

Accident Prevention↗
PubMed1999

Two-dimensional electrophoresis resources available from ExPASy.

This paper describes the set of two-dimensional electrophoresis (2-DE) resources currently available from the ExPASy proteomics Web server. These resources include the SWISS-2DPAGE database, 2-DE software packages, 2-DE technical and educational services, as well as indexes and search engines for 2-DE related sites over the Internet.

Databases, Factual↗
PubMed2003

Incorporating electronic media into medical student education: a survey of AMSER members on computer and web use in radiology courses. Alliance of Medical Student Educators in Radiology.

RATIONALE AND OBJECTIVES: The purpose of this study was to define the current use of information technology in radiology tutorials for medical students. MATERIALS AND METHODS: The authors conducted a Web-based survey of directors of medical school courses in radiology. The survey dealt with the details of the courses and the use of computers and the Web during the courses. RESULTS: There were 48 responses. Most radiology courses were elective (73%) and were offered monthly. Most institutions (79%) had picture archiving and communication systems (PACS) available or were completely filmless. The teaching case presentations, however, often included film images displayed on a view box or by an overhead projector. Computers dedicated to student use were uncommon (28%). The Web was used infrequently as a teaching resource, and a Web site was not available in most courses. Computer technical support was variable and usually provided by the course director. Course directors at institutions with PACS were more likely to use digital technology for case presentations and more likely to use the Web for teaching purposes. CONCLUSION: Despite the widespread use of digital technology and PACS in the field of radiology, digital technology is underused in radiology courses. However, departments with PACS tend to use digital technology more frequently in education than do departments without PACS.

Computer-Assisted Instruction↗
PubMed2000

Developing a value-added Web site.

Once a healthcare organization has decided to establish a Web site on the Internet, it must next determine its implementation strategy, based on a full understanding of the goals of the site and the range of Web content and service offerings available in the marketplace. Although some organizations may choose to develop and maintain a Web site using exclusively in-house resources, most healthcare organizations will find that they can minimize the costs associated with this effort by making judicious use of outsourcing services. Whichever approach is used, it is important that financial managers charged with allocating resources for Web-site development and maintenance understand the implications, including relative financial impact, of key issues and options.

Advertising↗
PubMed2006

Habitat connectivity and ecosystem productivity: implications from a simple model.

The import of resources (food, nutrients) sustains biological production and food webs in resource-limited habitats. Resource export from donor habitats subsidizes production in recipient habitats, but the ecosystem-scale consequences of resource translocation are generally unknown. Here, I use a nutrient-phytoplankton-zooplankton model to show how dispersive connectivity between a shallow autotrophic habitat and a deep heterotrophic pelagic habitat can amplify overall system production in metazoan food webs. This result derives from the finite capacity of suspension feeders to capture and assimilate food particles: excess primary production in closed autotrophic habitats cannot be assimilated by consumers; however, if excess phytoplankton production is exported to food-limited heterotrophic habitats, it can be assimilated by zooplankton to support additional secondary production. Transport of regenerated nutrients from heterotrophic to autotrophic habitats sustains higher system primary production. These simulation results imply that the ecosystem-scale efficiency of nutrient transformation into metazoan biomass can be constrained by the rate of resource exchange across habitats and that it is optimized when the transport rate matches the growth rate of primary producers. Slower transport (i.e., reduced connectivity) leads to nutrient limitation of primary production in autotrophic habitats and food limitation of secondary production in heterotrophic habitats. Habitat fragmentation can therefore impose energetic constraints on the carrying capacity of aquatic ecosystems. The outcomes of ecosystem restoration through habitat creation will be determined by both functions provided by newly created aquatic habitats and the rates of hydraulic connectivity between them.

Animals↗
PubMed2004

PhosphoSite: A bioinformatics resource dedicated to physiological protein phosphorylation.

PhosphoSite is a curated, web-based bioinformatics resource dedicated to physiologic sites of protein phosphorylation in human and mouse. PhosphoSite is populated with information derived from published literature as well as high-throughput discovery programs. PhosphoSite provides information about the phosphorylated residue and its surrounding sequence, orthologous sites in other species, location of the site within known domains and motifs, and relevant literature references. Links are also provided to a number of external resources for protein sequences, structure, post-translational modifications and signaling pathways, as well as sources of phospho-specific antibodies and probes. As the amount of information in the underlying knowledgebase expands, users will be able to systematically search for the kinases, phosphatases, ligands, treatments, and receptors that have been shown to regulate the phosphorylation status of the sites, and pathways in which the phosphorylation sites function. As it develops into a comprehensive resource of known in vivo phosphorylation sites, we expect that PhosphoSite will be a valuable tool for researchers seeking to understand the role of intracellular signaling pathways in a wide variety of biological processes.

Animals↗
PubMed2006

Consumer-resource body-size relationships in natural food webs.

It has been suggested that differences in body size between consumer and resource species may have important implications for interaction strengths, population dynamics, and eventually food web structure, function, and evolution. Still, the general distribution of consumer-'resource body-size ratios in real ecosystems, and whether they vary systematically among habitats or broad taxonomic groups, is poorly understood. Using a unique global database on consumer and resource body sizes, we show that the mean body-size ratios of aquatic herbivorous and detritivorous consumers are several orders of magnitude larger than those of carnivorous predators. Carnivorous predator-prey body-size ratios vary across different habitats and predator and prey types (invertebrates, ectotherm, and endotherm vertebrates). Predator-prey body-size ratios are on average significantly higher (1) in freshwater habitats than in marine or terrestrial habitats, (2) for vertebrate than for invertebrate predators, and (3) for invertebrate than for ectotherm vertebrate prey. If recent studies that relate body-size ratios to interaction strengths are general, our results suggest that mean consumer-resource interaction strengths may vary systematically across different habitat categories and consumer types.

Animals↗
PubMed2000

Variance in ecological consumer-resource interactions.

Food-web models use the effect size of trophic interactions to predict consumer-resource dynamics. These models anticipate that strong effects of consumers increase spatial and temporal variability in abundance of species, whereas weak effects dampen fluctuations. Empirical evidence indicates that opposite patterns may occur in natural assemblages. Here I show that spatial variance in the distribution of resource populations is sensitive to changes in the variance of the trophic interaction, in addition to the mean effect of consumers, relative to other causes of spatial variability. Simulations indicate that both strong and weak direct effects of consumers can promote spatial variability in abundance of resources, but only trophic interactions with a large mean effect size can reduce variation. Predictions of the model agree with the results of repeated field experiments and are consistent with data from published consumer-resource interactions, proving to be robust across widely varying environmental conditions and species' life histories. Thus, food-web models that embody variance in trophic interactions may have increased capacity to explain the wide range of effects of consumers documented in empirical studies.

Ecology↗
PubMed2006

MACiE (Mechanism, Annotation and Classification in Enzymes): novel tools for searching catalytic mechanisms.

MACiE (Mechanism, Annotation and Classification in Enzymes) is a database of enzyme reaction mechanisms, and is publicly available as a web-based data resource. This paper presents the first release of a web-based search tool to explore enzyme reaction mechanisms in MACiE. We also present Version 2 of MACiE, which doubles the dataset available (from Version 1). MACiE can be accessed from http://www.ebi.ac.uk/thornton-srv/databases/MACiE/

Catalysis↗
PubMed2006

CROPPER: a metagene creator resource for cross-platform and cross-species compendium studies.

BACKGROUND: Current genomic research methods provide researchers with enormous amounts of data. Combining data from different high-throughput research technologies commonly available in biological databases can lead to novel findings and increase research efficiency. However, combining data from different heterogeneous sources is often a very arduous task. These sources can be different microarray technology platforms, genomic databases, or experiments performed on various species. Our aim was to develop a software program that could facilitate the combining of data from heterogeneous sources, and thus allow researchers to perform genomic cross-platform/cross-species studies and to use existing experimental data for compendium studies. RESULTS: We have developed a web-based software resource, called CROPPER that uses the latest genomic information concerning different data identifiers and orthologous genes from the Ensembl database. CROPPER can be used to combine genomic data from different heterogeneous sources, allowing researchers to perform cross-platform/cross-species compendium studies without the need for complex computational tools or the requirement of setting up one's own in-house database. We also present an example of a simple cross-platform/cross-species compendium study based on publicly available Parkinson's disease data derived from different sources. CONCLUSION: CROPPER is a user-friendly and freely available web-based software resource that can be successfully used for cross-species/cross-platform compendium studies.

Animals↗
PubMed2005

Web services and workflow management for biological resources.

BACKGROUND: The completion of the Human Genome Project has resulted in large quantities of biological data which are proving difficult to manage and integrate effectively. There is a need for a system that is able to automate accesses to remote sites and to "understand" the information that it is managing in order to link data properly. Workflow management systems combined with Web Services are promising Information and Communication Technologies (ICT) tools. Some have already been proposed and are being increasingly applied to the biomedical domain, especially as many biology-related Web Services are now becoming available. Information on biological resources and on genomic sequences mutations are two examples of very specialized datasets that are useful for specific research domains. RESULTS: The architecture of a system that is able to access and execute predefined workflows is presented in this paper. Web Services allowing access to the IARC TP53 Mutation Database and CABRI catalogues of biological resources have been implemented and are available on-line. Example workflows which retrieve data from these Web Services have also been created and are available on-line. CONCLUSION: We present a general architecture and some building blocks for the implementation of a system that is able to remotely execute workflows of biomedical interest and show how this approach can effectively produce useful outputs. The further development and implementation of Web Services allowing access to an exhaustive set of biomedical databases and the creation of effective and useful workflows will improve the automation of in-silico analysis.

Animals↗
PubMed1996

Efficient searching for specific resources on the World-Wide Web: creation of a search server for radiologists.

OBJECTIVE: Our objective was to develop an efficient way to search for radiology information on the World-Wide Web (WWW). MATERIALS AND METHODS: With the Harvest Information Discovery and Access System and a DECstation 3000 computer, each week we gather and update WWW documents that relate to radiology. To limit the size of the gathered documents, certain data (such as image files) are omitted. To date, we have gathered from 20 main radiology sites. By accessing our server, thousands of documents can be efficiently searched for specific radiology information. RESULTS: At no charge, individuals with access to the WWW can request a search of our server for specific radiology information. We return to the requester in HyperText Markup Language a document with results of the search included as embedded pointers. Our server address, or uniform resource locator, is http://glimpse.cs.arizona.edu/radiology.html. CONCLUSION: Use of a server dedicated to radiology is an efficient way to search the internet for radiology resources, such as teaching files. We provide access to many sites with one search, and we select those sites to ensure that only relevant and timely information is gathered. We also index that information.

Computer Communication Networks↗
PubMed2006

Informatics-based learning resources for patients and their relatives in recovery.

In this paper we describe experiences from design of an informatics-based learning resource for patients and relatives. The prototype, REPARERE (learning REsource for PAtients and RElatives during REcovery), aims to support patients and their family recovering from heart surgery in meeting challenges in to daily living post discharge. Using recovery experiences and patient teaching material, REPARERE includes examples of textual information, video-clips, images and illustrations relevant to the recovery trajectory and a user's digitally represented profile. The development of the prototype focuses on flexibility and usability, tailoring and sequencing resources, and inclusion of recommendations for universal access. Development of web-based learning resources allows for exploration of 'just-in-case' and 'just-in-time' strategies to information retrieval and knowledge construction in health and learning trajectories. Findings from the literature, discussions with patients as well as health care providers indicate that unfulfilled information needs in the recovery period are common. Resources like REPARERE would be valuable supplement to facilitate patient learning about symptom management, self-care and coping while recovering.

Family↗
PubMed2006

Database resources of the National Center for Biotechnology Information.

In addition to maintaining the GenBank nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources for the data in GenBank and other biological data made available through NCBI's Web site. NCBI resources include Entrez, the Entrez Programming Utilities, My NCBI, PubMed, PubMed Central, Entrez Gene, the NCBI Taxonomy Browser, BLAST, BLAST Link(BLink), Electronic PCR, OrfFinder, Spidey, Splign, RefSeq, UniGene, HomoloGene, ProtEST, dbMHC, dbSNP, Cancer Chromosomes, Entrez Genome, Genome Project and related tools, the Trace and Assembly Archives, the Map Viewer, Model Maker, Evidence Viewer, Clusters of Orthologous Groups (COGs), Viral Genotyping Tools, Influenza Viral Resources, HIV-1/Human Protein Interaction Database, Gene Expression Omnibus (GEO), Entrez Probe, GENSAT, Online Mendelian Inheritance in Man (OMIM), Online Mendelian Inheritance in Animals (OMIA), the Molecular Modeling Database (MMDB), the Conserved Domain Database (CDD), the Conserved Domain Architecture Retrieval Tool (CDART) and the PubChem suite of small molecule databases. Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized data sets. These resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov.

Animals↗
PubMed2006

Database resources of the National Center for Biotechnology Information.

In addition to maintaining the GenBank nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources for the data in GenBank and other biological data made available through NCBI's Web site. NCBI resources include Entrez, the Entrez Programming Utilities, MyNCBI, PubMed, PubMed Central, Entrez Gene, the NCBI Taxonomy Browser, BLAST, BLAST Link (BLink), Electronic PCR, OrfFinder, Spidey, Splign, RefSeq, UniGene, HomoloGene, ProtEST, dbMHC, dbSNP, Cancer Chromosomes, Entrez Genomes and related tools, the Map Viewer, Model Maker, Evidence Viewer, Clusters of Orthologous Groups, Retroviral Genotyping Tools, HIV-1, Human Protein Interaction Database, SAGEmap, Gene Expression Omnibus, Entrez Probe, GENSAT, Online Mendelian Inheritance in Man, Online Mendelian Inheritance in Animals, the Molecular Modeling Database, the Conserved Domain Database, the Conserved Domain Architecture Retrieval Tool and the PubChem suite of small molecule databases. Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized datasets. All of the resources can be accessed through the NCBI home page at: http://www.ncbi.nlm.nih.gov.

Databases, Genetic↗