In This Issue

This issue contains two reviews, one on the findings from high-risk studies of schizophrenia, and one comparing two psychological interventions for post-traumatic stress disorder (PTSD). Other sets of papers examine various aspects of PTSD, psychosis, personality disorder, and common mental disorders, and four individual papers examine a variety of topics.


Conference Report
Pierre-Alain Binz et al. and Antoine de Daruvar provide an in-depth report on the meeting, including some interesting insights from the discussion sessions.

Conference Reviews
Denis Shields and Aisling O'Halloran review the considerations for integrating genotypic data with transcriptomic and proteomic data. These highthroughput approaches have the potential to identify the consequences of genetic variability. Studies combining these methods with genetic analyses could advance our understanding of the genetic aetiology of complex disorders Francisco Azuaje gives us an overview of the problems currently being investigated by the computational intelligence community in working towards the semantic web, and discusses the potential for machine learning to aid the integration of data in the post-genomics era.
Uwe Kärst et al. describe the REALIS project, for post-genomic analysis of the food-born pathogen Listeria monocytogenes. The consortium is organised into work packages covering transcriptome and proteome profiling, analysis of regulatory elements, mutagenesis, comparative genomics and bioinformatics.
Peter Rice et al. present RibDB, an SRS-based database designed to meet the requirements of the REALIS consortium. RibDB integrates consortium data with that from public databases and provides a range of analysis applications to consortium members.
Colin Harwood and Ivan Moszer describe the BACELL project, for functional genomics of Bacillus subtilis. This project is generating data from a variety of functional genomics projects and gene regulation programmes. This data needs to be integrated with the vast array of biochemical and physiological data already available on this interesting bacterium. They discuss the challenges ahead and the work undertaken so far to meet them.
In his review on ontology-based document enrichment in bioinformatics, Robert Stevens discusses the uses of controlled vocabularies and how they can increase the utility of documents by making them computationally accessible.
Henning Hermjakob and Rolf Apweiler present Temblor, an EU funded project, which will provide an integrated view of genomic and proteomic data, drawn from databases across Europe. This will include the creation of new resources for protein interaction, structural and microarray data.

Section on Pharmacogenetics
Pyrosequencing for SNP detection Mostafa Ronaghi and Elahe Elahi discuss the application of Pyrosequencing technology to mutation scanning, SNP discovery, and haplotyping.

High-throughout SNP genotyping technologies
Suzanne Jenkins and Tim Gibson discuss the advantages and drawbacks of the chemistries and platforms available for high-throughput SNP genotyping. They also discuss potential routes to future increases in throughput. This is a critical requirement for whole genome approaches using SNPs, which could transform complex disease genetics and expedite pharmacogenetics research. Comp Funct Genom 2002;3: 1-2. DOI: 10.1002 / cfg.142 SNP and Mutation data on the Web Mike Barnes reviews the resources currently available on the Internet for working with SNPs and mutations. There are two main databases acting as SNP repositories, dbSNP and HGBASE, which have different approaches, but do synchronise their datasets. There are also tools for SNP visualisation and mapping, including Ensembl and LocusLink. The mutation databases HGMD, OMIM and GDB are also profiled.

Website Update: JEMBOSS
Tim Carver and Lisa Mullan present JEMBOSS, a Java interface for EMBOSS (The European Molecular Biology Open Software Suite). This suite of tools ranges from motif searches and sequence alignments to phylogenetic analyses and structural predictions.

2
In this Issue