Copyright©2008 Antony Williams
We are progressing quite well with our development of Chemmantis, the document markup system for Chemistry-related documents. One of the problems with marking up various types of chemical entity is how “colorful” they can become as you markup a document. Some examples of markup we are considering are shown in the image. Not all of the supporting dictionaries are in place yet but are under development.
If you consider a standard chemistry document with the number of chemicals, reactions, elements and groups that can show up in just a paragraph you can end up with the “Christmas Tree effect”. An example of the effect is shown below. There are actually only three colors/effects shown – mark up of chemical names, mark up of elements and mark up of chemical names with no associated structure…in this case Bis-pi-allylnickel.
So, all elements are marked separately and, using the check box capability in the floating window, can be switched on and off. believe me, you need this. The words carbon, oxygen, nitrogen and hydrogen, for example, show clearly will up a lot in chemistry articles (hydrogen bond, carbon-carbon bond etc). So, there are many cases where you would just want to switch the element view off. One check box and its done. the same is true for chemical names, species and, shortly, chemical groups and reaction types. We are also working on splitting out bacteria, fungi, viruses etc.
If you want to see where we are at present I encourage you to look at this IUPAC Pure and Applied Chemistry article entitled : Carbon-Carbon Bond Forming Reactions Using Alkyl Fluorides. The markup does not yet work in any browser other than Internet Explorer so try it there. Hover over the chemical names and you should see the chemical balloon show up as shown below. In the next few days we hope to roll out the connections out to related data from this structure balloon. Watch this space.Stumble it!