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{bio,medical} informatics

Wednesday, March 28, 2001

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find related articles. powered by google. BioMedNet New consortium to put microarray data into your hands
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"Leaders of an effort to standardize and centralize gene expression data on tumor samples today described their vision for an international non-profit consortium to make such microarray data available to all researchers. The non-governmental project aims to increase the rate of discovery and improve patient care, said Jeffrey Trent, scientific director of the National Human Genome Research Institute speaking at the American Association for Cancer Research conference in New Orleans."
redux [05.24.00]
find related articles. powered by google. Nature One-stop shop for microarray data
"With the advent of DNA microarray and 'chip' technologies...gene expression in an organism can be examined on a genomic scale, allowing the transcription levels of many genes to be measured simultaneously2. For instance, we can study the effects of a compound (such as a drug) on the level of expression of many genes...With gene expression, context is everything: without it, the information is meaningless. For example, the precise stage of a tumour sample could have a crucial bearing on the interpretation of expression measurements. This context can be infinitely detailed, and it is this detail that must be captured in gene-expression studies.

The bioinformatics underlying the management of these huge volumes of data are crucial if any sense is to be made of gene-expression experiments. A single microarray experiment looking at 40,000 genes from 10 different samples, under 20 different conditions, produces at least 8,000,000 pieces of information."

"It is time to create a public repository for microarray data, with standardized annotation (see Box 2, overleaf). But this is a complex and ambitious project, and is one of the biggest challenges that bioinformatics has yet faced. Major difficulties stem from the detail required to describe the conditions of an experiment, and the relative and imprecise nature of measurements of expression levels. The potentially huge volume of data only adds to these difficulties. However, it is this very complexity that makes an organized repository necessary.

Important tasks to be undertaken include: (1) agreement on the essential information that should be reported for a microarray experiment; (2) definition of ontologies and an extensible, structured document format to capture these data and their semantics; (3) production of a database to store these documents; and (4) development of tools for searching documents in a database and using the semantic context to allow comparisons and sophisticated queries."

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Bioinformatics will be at the core of biology in the 21st century. In fields ranging from structural biology to genomics to biomedical imaging, ready access to data and analytical tools are fundamentally changing the way investigators in the life sciences conduct research and approach problems. Complex, computationally intensive biological problems are now being addressed and promise to significantly advance our understanding of biology and medicine. No biological discipline will be unaffected by these technological breakthroughs.


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