MyWEST: my Web Extraction Software Tool for effective mining of annotations from web-based databanks

MOTIVATION: High-throughput technologies create the necessity to mine large amounts of gene annotations from diverse databanks, and to integrate the resulting data. Most databanks can be interrogated only via Web, for a single gene at a time, and query results are generally available only in the HTML format. Although some databanks provide batch retrieval of data via FTP, this requires expertise and resources for locally reimplementing the databank. RESULTS: We developed MyWEST, a tool aimed at researchers without extensive informatics skills or resources, which exploits user-defined templates to easily mine selected annotations from different Web-interfaced databanks, and aggregates and structures results in an automatically updated database. Using microarray results from a model system of retinoic acid-induced differentiation, MyWEST effectively gathered relevant annotations from various biomolecular databanks, highlighted significant biological characteristics and supported a global approach to the understanding of complex cellular mechanisms. AVAILABILITY: MyWEST is freely available for non-profit use at http://www.medinfopoli.polimi.it/MyWEST/     

Wrapping SRS with CORBA: from textual data to distributed objects.

MOTIVATION: Biological data come in very different shapes. Databanks are maintained and used by distinct organizations. Text is the de facto Standard exchange format. The SRS system can integrate heterogeneous textual databanks but it was lacking a way to structure the extracted data. RESULTS: This paper presents a CORBA interface to the SRS system which manages databanks in a flat file format. SRS Object Servers are CORBA wrappers for SRS. They allow client applications (visualisation tools, data mining tools, etc.) to access and query SRS servers remotely through an Object Request Broker (ORB). They provide loader objects that contain the information extracted from the databanks by SRS. Loader objects are not hard-coded but generated in a flexible way by using loader specifications which allow SRS administrators to package data coming from distinct databanks. AVAILABILITY: The prototype may be available for beta-testing. Please contact the SRS group (http://srs.ebi.ac.uk).     

MPSA: integrated system for multiple protein sequence analysis with client/server capabilities

SUMMARY: MPSA is a stand-alone software intended to protein sequence analysis with a high integration level and Web clients/server capabilities. It provides many methods and tools, which are integrated into an interactive graphical user interface. It is available for most Unix/Linux and non-Unix systems. MPSA is able to connect to a Web server (e.g. http://pbil.ibcp.fr/NPSA) in order to perform large-scale sequence comparison on up-to-date databanks. AVAILABILITY: Free to academic http://www.ibcp.fr/mpsa/ CONTACT: c.blanchet@ibcp.fr     

A gentle introduction to SNP analysis: resources and tools

Bioinformatics is the use of informatics tools and techniques in the study of molecular biology, genetic, or clinical data. The field of bioinformatics has expanded tremendously to cope with the large expansion of information generated by the mouse and human genome projects, as newer generations of computers that are much more powerful have emerged in the commercial market. It is now possible to employ the computing hardware and software at hand to generate novel methodologies in order to link data across the different databanks generated by these international projects and derive clinical and biological relevance from all of the information gathered. The ultimate goal would be to develop a computer program that can provide information correlating genes, their single nucleotide polymorphisms (SNPs), and the possible structural and functional effects on the encoded proteins with relation to known information on complex diseases with great ease and speed. Here, the recent developments of available software methods to analyze SNPs in relation to complex diseases are reviewed with emphasis on the type of predictions on protein structure and functions that can be made. The need for further development of comprehensive bioinformatics tools that can cope with information generated by the genomics communities is emphasized.     

Bringing sequences to life: how bioinformatics corporealizes sequence data

Sequence databases have become more visible through the heavy publicity associated with the Human Genome Project. This paper looks at some of the emerging artefacts and systems developed to read, write, order and visualise sequence data and other kinds of biological data retrieved from databases and databanks such as GenBank. It argues that bioinformatics software can be regarded as a symptom of a broad and powerful transformation in biological knowledges and in the biopolitical constitution of living bodies. Two facets of this transformation are emphasised. Firstly, examining bioinformatics software might help us situate how sequence data is actually circulating, and to what ends. In particular, the paper looks at the significance of sequence comparison and protein folding problems. Secondly, an emerging nexus of property relations and intellectual work can be detected within the ordering of sequence data carried out bioinformatics.     

Measuring effectiveness of drugs in observational databanks: promises and perils

Observational databanks have inherent strengths and shortcomings. As in randomized controlled trials, poor design of these databanks can either exaggerate or reduce estimates of drug effectiveness and can limit generalizability. This commentary highlights selected aspects of study design, data collection and statistical analysis that can help overcome many of these inadequacies. An international metaRegister and a formal mechanism for standardizing and sharing drug data could help improve the utility of databanks. Medical journals have a vital role in enforcing a quality checklist that improves reporting.