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An introduction to BSML: enabling the bioinformatics revolution. (XML Labs).

Article Excerpt
Over the past two decades, the life sciences industry I has taken a dramatic leap into an online, collaborative world. Tasks and activities that are commonplace today were either extremely difficult or outright impossible just 20 years ago.

One key reason for this shift was the abundance of genomic sequence data, the sequence of base pairs that make up an organism's DNA. A vast amount of this data was made possible by advances in genomic sequencing techniques, such as the shotgun and clone contig techniques made famous to the general public during the Human Genome Project. In order to provide access to all of this publicly available data, the National Institute of Health created GenBank, an online repository of genomic information. When GenBank first opened in 1982 there were just 606 sequences available. Today, there are nearly 15 million sequences available--the number has doubled nearly every year since 1992!

With this vast amount of publicly available information came the need to share, organize, and analyze it. Bioinformatics was the term coined to describe this science. While bioinformatics is not an extremely well-defined term, in general it refers to three broad areas: the collection of new genomic data, the analysis and interpretation of existing data, and the development of new algorithms for analysis.

While the Interact has always been an important tool for researchers, it was a key catalyst for the bioinformatics revolution. Through the Interact, scientists we/e able to publish and analyze data in a truly collaborative fashion. One group of researchers could analyze a specific genome in a particular way to gain insight as to its function. They could then describe their new understanding of the genome sequence by annotating it and sharing that annotation. Research groups could then leverage the ongoing work of other groups through public data repositories. However, as with many areas on the Internet, a common format was required in order to efficiently share information.

Entrez XML

Early on, flat file formats were the de facto standard for information exchange. However, the larger the variety of information, the more difficult it became to capture it all. No longer was information sharing limited to the familiar raw genomic strings of A, T, C, and G. Broader annotations, research protocols, published research results, metabolic pathways, and more now needed to be shared and cross-referenced.

From its inception GenBank standardized on a format known as ASN.1. In fact, the ASN.1 format is still used by several large government organizations, including GenBank, as a default format. It is an object-oriented, text-based language that in many ways resembles XML. However, with the advent of XML it became apparent that XML would become the backbone of a future standard. Not only could XML represent arbitrarily complex information,...