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PubChem – Making Chemical Information Open

A Eurekalert report discusses the topic of PubChem, a database I mentioned last year in a Nature news item.

This time, the issue is more contentious than an announcement of how useful such a database might be as certain toes in the profit-making-not-for-profit sector have been trod on.

According to my good friends Peter Murray-Rust and Henry Rzepa, an XML-based approach to the communication of chemical information in the biomedical literature would prevent the loss of crucial information and facilitate the re-use of data and would be easily achievable using existing open tools and resources. They have published a commentary article in the Open Access journal BMC Bioinformatics arguing that it is time chemistry followed in the footsteps of bioinformatics and structural biology and moved towards the creation of an open semantic web facilitating access to chemical information.

PMR of the University of Cambridge, John Mitchell and Henry Rzepa of Imperial College London argue using three case studies that conventional methods such as cutting-and-pasting chemical information are time-consuming and introduce errors. The authors argue in favour of an open XML architecture linking to connection tables or open databases such as PubChem, to identify chemical compounds mentioned in the biomedical literature. Their article thus provides additional support for open chemical databases like PubChem, which is currently at the centre of a legal battle between the NIH and the American Chemical Society (ACS).

The chemists explain that an open XML-based architecture would provide a cost-effective and user-friendly way to publish chemical information.

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