Mark D. Wilkinson

Tag clouds for summarizing web search results

In this paper, we describe an application, PubCloud that uses tagclouds for the summarization of results from queries over thePubMed database of biomedical literature. PubCloud responds toqueries of this database with tag clouds generated from wordsextracted from the abstracts returned by the query. The results ofa user study comparing the PubCloud tag-cloud summarization ofquery results with the standard result list provided by PubMedindicated that the tag cloud interface is advantageous in presenting descriptive information and in reducing user frustrationbut that it is less effective at the task of enabling users to discoverrelations between concepts.

Semi-automatic web service composition for the life sciences using the BioMoby semantic web framework

Researchers in the life-sciences are currently limited to small-scale informatics experiments and analyses because of the lack of interoperability among life-sciences web services. This limitation can be addressed by annotating services and their interfaces with semantic information, so that interoperability problems can be reasoned about programmatically. The Moby semantic web framework is a popular and mature platform that is used for this purpose. However, the number of services that are available to select from when building a workflow is becoming unmanageable for users. As such, attempts have been made to assist with service selection and composition. These tasks fall under the general label of automated service composition. We present a prototype workflow assembly client that reduces the number of choices that users have to make by (1) restricting the overall set of services presented to them and (2) ranking services so that the the most desirable ones are presented first. We demonstrate via an evaluation of this prototype that a unification of relatively simple techniques can rank desirable services highly while maintaining interactive response times.

iHOPerator: user-scripting a personalized bioinformatics Web, starting with the iHOP website

BackgroundUser-scripts are programs stored in Web browsers that can manipulate the content of websites prior to display in the browser. They provide a novel mechanism by which users can conveniently gain increased control over the content and the display of the information presented to them on the Web. As the Web is the primary medium by which scientists retrieve biological information, any improvements in the mechanisms that govern the utility or accessibility of this information may have profound effects. GreaseMonkey is a Mozilla Firefox extension that facilitates the development and deployment of user-scripts for the Firefox web-browser. We utilize this to enhance the content and the presentation of the iHOP (information Hyperlinked Over Proteins) website.ResultsThe iHOPerator is a GreaseMonkey user-script that augments the gene-centred pages on iHOP by providing a compact, configurable visualization of the defining information for each gene and by enabling additional data, such as biochemical pathway diagrams, to be collected automatically from third party resources and displayed in the same browsing context.ConclusionThis open-source script provides an extension to the iHOP website, demonstrating how user-scripts can personalize and enhance the Web browsing experience in a relevant biological setting. The novel, user-driven controls over the content and the display of Web resources made possible by user-scripts, such as the iHOPerator, herald the beginning of a transition from a resource-centric to a user-centric Web experience. We believe that this transition is a necessary step in the development of Web technology that will eventually result in profound improvements in the way life scientists interact with information.

Vcsa1 gene peptides for the treatment of inflammatory and allergic reactions.

The recently emerged Vcsa1 gene is one member of the variable coding sequence (VCS) multigene family of Rattus norvegicus. This gene encodes the precursor prohormone SMR1 (submandibular rat-1), which on enzymatic processing gives rise to several 5 to 11 amino acid peptides that modulate a variety of physiological functions. The analgesic pentapeptide sialorphin and anti-inflammatory heptapeptide submandibular gland peptide-T (TDIFEGG) are the most intensively studied. Although the Vcsa1 gene and its protein product are unique to rats, TDIFEGG or a derivative acts on all species examined to date, including human cells, in functions related to allergic reactions and inflammation. In this review, the patent and academic literature on SMR1 and its natural peptides and their derivatives are reviewed for consideration of biological targets and relevance to the development of novel therapeutic agents. The VCS gene family is discussed and we speculate on possible human homologs of these potent anti-inflammatory rat-derived peptides. The biologically active peptide products of SMR1 are considered and the mechanism of action and structure-activity relationships of the anti-inflammatory submandibular gland peptide-T and its derivatives are discussed.

OWL2Perl: Creating Perl modules from OWL class definitions

Summary: Support for utilizing OWL ontologies in Perl is extremely limited, despite the growing importance of the Semantic Web in Healthcare and Life Sciences. Here, we present a Perl framework that generates Perl modules based on OWL Class definitions. These modules can then be used by other software applications to create resource description framework (RDF) data compliant with these OWL models. Availability: OWL2Perl is available for download from CPAN, under the module name OWL2Perl. It is released under the new BSD license. Contact: edward.kawas@gmail.com; markw@illuminae.com