8.1 Why using databases programmatically?

Information is essential to many professions and chemistry is no exception. As chemists we frequently have to look up chemical information in handbooks or databases; you can name it: formation enthalpies and entropies, solubilities, ionization constants, densities of mixtures, spectra...

Much of this information, although available, is spread among several handbooks, databases and/or papers in scientific journals. Sometimes we are able to find the information in well organized data sources and occasionally these are available online and can be accessed programmatically.

When this is the case, accessing these resources programmatically offers the following advantages:

●Availability and convenience. Curated and updated information is at your fingerprints. The information can be retrieved from your computer or your mobile device without requiring heavy applications or huge databases.
●Economy. Many of these sources offers data on licensing options that allow using it at no-cost in different contexts and environments.
●Knowledge and data sharing, reusing and repurposing. Many of the sources that are available fit onto the open access policies which are slowly being adopted by the scientific communities. Likewise, this open data allows you to build other applications and personal mashups.

Some example projects that make use of open databases are:

●Jmol: an open-source Java viewer for chemical structures in 3D. http://www.jmol.org/
●JSmol: an open-source HTML5 viewer for chemical structures in 3D. http://wiki.jmol.org/index.php/JSmol
●Open Notebook Science Web Services. http://onswebservices.wikispaces.com/
●SpectralGame. http://lxsrv7.oru.edu/~alang/
●MolView. http://molview.org/
●CheMagic. http://chemagic.com/molecules/VMKMINInotes.htm

AnchorFurther reading

●O'Boyle, N. M., Guha, R., Willighagen, E. L., Adams, S. E., Alvarsson, J., Bradley, J. C., ... & Murray-Rust, P. (2011). Open Data, Open Source and Open Standards in chemistry: The Blue Obelisk five years on. J. Cheminformatics, 3, 37. Available at http://www.biomedcentral.com/content/pdf/1758-2946-3-37.pdf

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