Recently, I wrote a tutorial on embedding 2-D molecular renderings into webpages as Scalable Vector Graphics (SVG). This tutorial also contained a small experiment on the current chemical informatics capabilities of the Web. Here is a scenario from the near future: Joe is writing a review on Cephalosporin C that he wants to publish the modern way - directly to the Web. An entirely new concept in scientific publishing has started to take hold.

Nomenclature translation is the process of converting a human-readable chemical name into a machine-readable notational scheme such as a connection table. It plays a key role in linking the older chemical literature to modern information technologies, such as the Internet. Buried deep within the Chemistry Development Kit (CDK) is a library for nomenclature translation called ChemNomParse.

Systematic nomenclature is one of the oldest forms of line notation. As a result, it can be found widely in papers, patents, spreadsheets, and other documents. Any software that can convert systematic nomenclature, such as IUPAC names, into a computer-based representational system, such as a connection table, has the potential to unlock vast amounts of legacy chemical information by making it structure-searchable.

A previous article showed some examples of 2-D molecular rendering using Scalable Vector Graphics (SVG) embedded in a web page. This article will outline some simple steps for generating these images and publishing them on the Web. Prerequisites This tutorial uses Structure-CDK, a CDK add-on library written in Java.

Until 1966, Chemical Abstracts Service used volunteers exclusively to abstract the chemical literature. At the system’s peak, thousands of scientists were willing and even enthusiastic to perform this tedious, demanding work for very little pay. The system was eventually phased out in favor of the professional abstracting service that replaced it. What motivated these volunteer abstracters? Enlightened self-interest probably played a role.

Scalable Vector Graphics (SVG) is an XML-based language for encoding graphical content. Unlike raster image formats such as PNG, JPEG, and GIF, SVG images can be scaled to any resolution without pixelation. Given that 2-D structure diagrams are essentially line drawings, SVG seems like a natural fit for this type of representation. SVG also boasts several advanced features that make it an especially intriguing choice.

The success of any new molecular encoding method relies, in part, on its invisibility to its prospective users. After all, why should anyone bother to learn yet another molecular language, especially one designed with computers in mind? Yet these encoding systems are critical in connecting chemical information and information technologies. How can any new encoding method be made part of existing workflows invisibly?

NMRShiftDB is an open web database of peer-reviewed NMR chemical shifts compiled by volunteers. As of this writing, it contains 22,429 measured spectra from 18,986 structures, and reports 927 registered users. The database code itself is open source.

Fugmann goes on to observe some other points that distinguish chemical information from the information of other fields: It’s Hard for Computers to Deal with Chemical Structures. The chemical structure may be a universally understandable language for humans, but not for computers. Searching for chemical structures requires much more advanced and computationally intensive technologies than searching for text.

Line notations are useful for encoding molecular structure with computers, especially in a network environment. Because line notations are compact and ASCII-based, they can, among other purposes, be used to query popular Web search engines for chemical content on the web.

PubChem is an increasingly popular, free-access, online molecular database operated by the National Institutes of Health. Web services are a hot topic, with sites such as Flickr, Google, and eBay offering developers the tools to build rich content through “mashups” of several web APIs. Although there is no formal PubChem API, it’s possible to roll your own.