IUPAC/InChI joins the Microsoft BioIT Alliance

On the CHMINF-L mailing list it was reported that the IUPAC InChI/InChIKey project joins Microsoft BioIT Alliance. Quoting:

The establishment of the BioIT Alliance in April 2006 by Microsoft and leading organizations in the life science industries was very much a reflection of this scenario, and the Alliance has now been extended to include a major Scientific Union, the International Union of Pure and Applied Chemistry (IUPAC). The importance of IUPACs contribution to the enterprise lies primarily in the responsibility of this organization for establishing standards for transmitting chemical information.

I am political quite illiterate, and have no idea why the BioIT Alliance could not use InChI or InChIKey without this mashup. However, I am comforted in the knowledge that the IUPAC InChI/InChIKey project will make sure the Microsoft will not use the InChIKey as drug identifier, which would give very nice (but letal) Millenium-bug like situations when that unlike key clash was found ;)

More molecules in Cb

Because the use of chemical microformats and RDFa is not yet picking up, I extended Cb to detect molecules via Wikipedia. This is paying off, even though a lot of Wikipedia entries do not list InChIs: the list is much longer now, and covers a much larger set of blogs. Thanx to all who link to Wikipedia when naming a chemical compound!

Special Markup Howto #1

Because the Postgenomic.com website has been rather slow for me (Euan, what is causing that? Too many users?), and upon user request, I start a series of Special Markup articles here, which will give the most up to date description of the supported markup.

Marking up Conferences
Conferences can be markup by using the @rel="conference" attribute for the <a> element. See an earlier blog item.

Marking up Articles
While the software will pick up most literature automatically, you can mark up a paper as being reviewed. Just add the @rel="review" attribute to the <a> element linking to the journal article webpage.

Marking up Molecules
This has been described in this earlier blog item. The softeware will pickup the markup for SMILES and InChI's.

Microformats
There are currently no microformats supported, but this is anticipated. For example, hCalender and hReview are likely candidates.

Latest blogged molecules on front page

I finally found a bit of time to further work on the molecules part of the postgenomic.com software, and replaced the 'hot tags' tab on the front page, by the eight latest blogged about molecules. Additionally, the system now allows deep linking to molecules in the database via the InChI, for example for N,N,N',N'-tetramethylnaphthalene-1,8-diamine [1]. This is what the front page now looks like:



1.InChI=1/C14H18N2/c1-15(2)12-9-5-7-11-8-6-10-13(14(11)12)16(3)4/h5-10H,1-4H3

Hacking InChI support into Cb

Ten months ago I wrote about Hacking InChI support into postgenomic.com. Since then, the PostGenomic.com software has seen a major update, which I recently followed. This means, that Chemical blogspace is now aggregating the compounds you blog about. That is, if you use the proper markup. At this moment, it only supports InChI and SMILES, as I have no means to deduce the molecular structure from a CAS registry number, and I have not integrated OPSIN yet.

Just to give the proper markup to trigger aggregation from your blog:

• for SMILES: <span xmlns:chem="http://www.blueobelisk.org/chemistryblogs/" class="chem:smiles">CCO</span>
• for InChI: <span xmlns:chem="http://www.blueobelisk.org/chemistryblogs/" class="chem:inchi">InChI=1/CH4/h1H4</span>

Here's the screenshot:

Note the PubChem and Google links created with a GreaseMonkey script I wrote.

Some future plans (other ideas are very much appreciated):

• OPSIN support for <span class="chem:compound">benzene</span>
• 2D diagrams on Cb
• Some details on the compound, maybe URLs?
• once the corpus is large enough, provide to PubChem
• extract more chemistry from blogs