Given the emergence of worldwide all-volunteer documentation efforts like Wikipedia, perhaps now is a good time to reconsider the feasibility of a very different form of all-volunteer chemical abstracting service. The all-volunteer system was used by CAS almost exclusively until 1966. Although these abstractors were called “volunteers”, they did receive a payment for their work - about $0.18/line in 1979.

Molecular line notations reduce a molecular structure to a string of ASCII characters. This is helpful in a variety of situations: as a method of text-based structure input; as a compact representation that can be stored and transmitted over a network; and in some cases as a method for uniquely identifying a molecular structure. The development of line notations is one of the oldest pursuits in chemical informatics.

Apparently, advances in chemical line notations have a history of occurring in clusters. Perhaps the development of InChI will spawn a renaissance in the development and use of line notations. Is there room (or need) for multiple line notation languages, each filling a particular niche, or can a universal line notation ever be developed?

Rino is a Ruby library for generating InChI identifiers. Currently, molfile input is supported. The following code illustrates basic usage.

If Mr Gushee was right, then why didn’t the system collapse under its own weight in the nearly 40 years since he wrote these words? Is it possible that calls for Open Access in scientific publishing are missing something fundamental in the culture of science? Why has the nature of scientific publishing changed so little in almost 300 years of continuous operation? Maybe revolutionary advances in information technology kept the system viable.

Ruby is a dynamic object oriented scripting language. First released in 1995 by a Japanese programmer, it has recently begun to attract a worldwide audience. The use of Ruby in chemical informatics, although currenly rare, can be expected to increase. One especially interesting project is ChemRuby. Although the website is written in Japanese, there is enough English to get a feel for what ChemRuby is all about.

Computers have been used to solve chemical informatics problems for a long time. Hardware and software have changed radically, but surprisingly, many of the most important problems of 1956 are still significant in 2006. Like many older information industries, chemical informatics has been dominated by a few big players for most of its existence.

The InChI canonicalization algorithm uniquely numbers the atoms of a molecule. To date, the only implementation is found in the C source code of the InChI software. To enable new InChI implementations, for example in other programming languges, the complete canonicalization procedure is needed. Although it has not been published formally, the information exists in two messages posted to the inchi-discuss mailing list by Dmitrii Tchekhovskoi.