The (my)Grid ontology: bioinformatics service discovery.

(my)Grid supports in silico experiments in the life sciences, enabling the design and enactment of workflows as well as providing components to assist service discovery, data and metadata management. The (my)Grid ontology is one component in a larger semantic discovery framework for the identification of the highly distributed and heterogeneous bioinformatics services in the public domain. From an initial model of formal OWL-DL semantics throughout, we now adopt a spectrum of expressivity and reasoning for different tasks in service annotation and discovery. Here, we discuss the development and use of the (my)Grid ontology and our experiences in semantic service discovery.

Cardiovascular risk assessment scoring system for the determination of cardiovascular mortality in renal transplant patients.

It is well known that the greatest risk for mortality post-renal transplant is cardiovascular death. We compared a modified cardiac risk assessment system among renal transplant patients who subsequently died versus the group that survived. There was a good correlation between the low, medium, and high scores with survival. The deceased group had significantly greater cardiovascular scores than case controls.

Exploring Williams-Beuren syndrome using myGrid.

MOTIVATION: In silico experiments necessitate the virtual organization of people, data, tools and machines. The scientific process also necessitates an awareness of the experience base, both of personal data as well as the wider context of work. The management of all these data and the co-ordination of resources to manage such virtual organizations and the data surrounding them needs significant computational infra-structure support. RESULTS: In this paper, we show that (my)Grid, middleware for the Semantic Grid, enables biologists to perform and manage in silico experiments, then explore and exploit the results of their experiments. We demonstrate (my)Grid in the context of a series of bioinformatics experiments focused on a 1.5 Mb region on chromosome 7 which is deleted in Williams-Beuren syndrome (WBS). Due to the highly repetitive nature of sequence flanking/in the WBS critical region (WBSCR), sequencing of the region is incomplete leaving documented gaps in the released sequence. (my)Grid was used in a series of experiments to find newly sequenced human genomic DNA clones that extended into these 'gap' regions in order to produce a complete and accurate map of the WBSCR. Once placed in this region, these DNA sequences were analysed with a battery of prediction tools in order to locate putative genes and regulatory elements possibly implicated in the disorder. Finally, any genes discovered were submitted to a range of standard bioinformatics tools for their characterization. We report how (my)Grid has been used to create workflows for these in silico experiments, run those workflows regularly and notify the biologist when new DNA and genes are discovered. The (my)Grid services collect and co-ordinate data inputs and outputs for the experiment, as well as much provenance information about the performance of experiments on WBS. AVAILABILITY: The (my)Grid software is available via http://www.mygrid.org.uk

A methodology to migrate the gene ontology to a description logic environment using DAML+OIL.

The Gene Ontology Next Generation Project (GONG) is developing a staged methodology to evolve the current representation of the Gene Ontology into DAML+OIL in order to take advantage of the richer formal expressiveness and the reasoning capabilities of the underlying description logic. Each stage provides a step level increase in formal explicit semantic content with a view to supporting validation, extension and multiple classification of the Gene Ontology. The paper introduces DAML+OIL and demonstrates the activity within each stage of the methodology and the functionality gained.

GALEN ten years on: tasks and supporting tools.

The GALEN technology has matured over more than a decade of use. We describe a set of software tools and associated methodologies that together are supporting ontological engineering in a production, rather than a research setting.

Integrating existing drug formulation terminologies into an HL7 standard classification using OpenGALEN.

Many terminologies exist for the form of drugs--i.e. tablets, capsules, sprays, suppositories, etc. However, they have surprisingly different content. To communicate medication messages effectively, a mechanism is needed to translate between these existing terminologies. An ontological approach, based on techniques developed by OpenGALEN, has been used to build a drug form terminology for HL7 version 3. It integrates existing terminologies from commercial drug information vendors and regulatory authorities, and provides a framework for translating between them. To date, term sets have been included from First DataBank, the FDA, Multum and Micromedex, to produce a terminology of 820 concepts. The approach is made practical by distributing the knowledge engineering effort to volunteers with experience of the domain, and then integrating the knowledge into a logically consistent classification.

Having our cake and eating it too: how the GALEN Intermediate Representation reconciles internal complexity with users' requirements for appropriateness and simplicity.

Clinical terminologies are complex objects, getting more complex as the requirements on them grow, and as more complex technologies are used in their construction. But to the clinical end-user, functionality and utility is important, not inherent complexity--the simpler a clinical terminology can be for the end-user, the better. To reconcile these contradictory requirements, the GALEN Programme has developed an Intermediate Representation that allows the OpenGALEN Clinical Terminology to retain a high degree of internal complexity, whilst allowing it to be efficiently maintained, and easily used. This paper describes the elements of the Intermediate Representation, how it works, and some experience of its use.

A reference terminology for drugs.

GALEN technology for re-usable terminologies using formal classification is being applied to the creation and maintenance of a reference terminology for drugs. GALEN's techniques are being used to address specific deficiencies of existing drug classifications that make it difficult to create and maintain guidelines to support prescribing in the care of patients with chronic diseases. The reference terminology is in two parts; firstly, a re-usable and automatically-classified 'ontology' is built with GALEN technology; this describes generic drugs, their composition in terms of chemicals and chemical classes, their actions, indications and interactions. Secondly, a 'dictionary' of prescribable proprietary products is integrated with this ontology. The result is a drug resource designed to support both the traditional uses of a drug knowledge base (e.g. prescribing and messaging), and the specialized demands of guideline authoring and execution.

Shared governance: time to consider the cons as well as the pros.

AIMS: This paper aims to provide a critical appraisal of an approach to the management and organization of nursing work known as shared governance (SG). BACKGROUND: This approach has its origins in the USA, where, during the past 20 years it has become increasingly influential. The advocates of SG claim that it can, inter alia, improve recruitment and retention rates, boost morale, and help raise clinical skills. Little wonder that SG in now beginning to make significant inroads into the NHS. ORIGIN OF INFORMATION: However, a trawl through the extensive US literature, using printed and online (e.g. BIDS, CINHAL, MEDLINE, etc.) bibliographical sources, suggests that the claimed benefits of SG should be treated with caution. KEY ISSUES: Much of the existing published research appears to be both methodologically flawed and lacking in any critical edge. While many researchers and commentators appear only too willing to highlight what they see as the promise of SG, they shy away from exploring any potential pitfalls. One consequence of this is that many of the putative benefits SG is said to confer, may in fact be more apparent than real. CONCLUSIONS: Nurses and nurse managers need to be apprised of and consider seriously, the possible cons as well as the potential pros of SG, if any promise it may have is to be realized.

Sequence elements involved in the rescue of IBV defective RNA CD-91.

Deletion mutagenesis has been used to identify essential regions for rescue of coronavirus defective RNAs (D-RNAs). Using this technique on a cloned IBV D-RNA CD-91, we have identified a region potentially important in its rescue. Comparing the sequence of D-RNAs rescued with those not rescued we have deduced that a 72 base region corresponding to base number 13,824 to 13,896 in the viral genome is required for rescue. This may be an IBV D-RNA packaging signal or a cis-acting element involved in replication. Further experiments and modification of our techniques will be required to differentiate between the two processes.