Chemical structures are a language. Like any language, grammar and spelling convey meaning and become “standardized” over time. But as native speakers of any language will tell you, languages also take on important cultural nuances that are difficult to convey to non-native speakers. Chemical structures are no different, as Stuart Cantrill’s comments show.
Yet another free chemistry database comes in the form of a service run by the journal Heterocycles . The Heterocycles Web Edition offers two ways to search for heterocylic ring systems: by structure or by synthesis. You may assume that these services would only search the contents of Heterocycles . It would then be a pleasant surprise to find a number of highly-regarded journals being covered. Here are some of titles: Angew.
Two recent J. Chem. Inf. Model. articles support the idea that PubChem is rapidly evolving into a Chemical Informatics platform: Large-Scale Annotation of Small-Molecule Libraries Using Public Databases. Using PubChem and other databases, the authors categorize the level of annotation (data, metadata, and links) of free chemical databases, with PubChem as the centerpiece.
Compiling and managing a bibliography is still a pain. The problem is that too many of the available tools require more busywork than necessary. Copying, pasting, and especially transcribing all fall into this category. And most tools fail to take advantage of the fact that the Web browser has become the de facto standard tool for scientific information gathering. A piece of software called Zotero may change this.
As work on the 2D chemical structure editor I’ve codenamed Firefly enters its finishing iteration, I’m reminded of the many things in life that seem to get exponentially more difficult the closer they get to completion. There should be a name for this effect. The closest thing I’ve seen to a discussion is Seth Godin’s The Dip. Although every project has its own unique qualities, they all tend to go through the same three stages.
Just ten years ago, the thought of accessing all of the world’s scientific literature online struck many as optimistic at best. Today, an increasing number of scientists use the Web as their only means of reading the literature.
SMILES and InChI are the two most widely-used line notations in cheminformatics. Not surprisingly, there are many situations in which it’s useful to interconvert the two. This article shows a simple method for doing so using Ruby Open Babel. Parsing InChIs Version 1.01 of the IUPAC/NIST C InChI toolkit introduced the ability to parse InChIs. This capability has subsequently been incorporated into Open Babel, and by extension, Ruby Open Babel.
CiteULike lets users easily manage their bibliographies of scholarly works, and in the process discover other users’ papers on related subjects. One of the most powerful features of CiteULike is its ability to convert arbitrary URLs into fully-formatted bibliographical citations. CiteULike manages to do this while largely avoiding the Buggotea Problem in which multiple URLs pointing to the same work are saved.
Have you ever wanted to find a molecule on the Web using your favorite search engine in combination with a 2-D structure editor? InChIMatic is a service that lets you do just that. In this article, I’ll show how InChIMatic can be used to look up molecules in the UsefulChem-Molecules blog.
It turns out the world was a lot messier than it seemed - and it’s about time. I couldn’t help but be reminded of The Long Tail as I watched this presentation by David Weinberger. Ein Fehler ist aufgetreten. Sieh dir dieses Video auf www.youtube.com an oder aktiviere JavaScript, falls es in deinem Browser deaktiviert sein sollte. Thanks to Richard Cameron of CiteULike for the link.
I realize that being the U.S. Government has its advantages, but the copyright notice at the bottom of a recent J. Chem. Inf. Model. paper caught my attention: As far as I can tell, this article is not part of the ACS AuthorChoice program.
