I will likely populate it a bit more soon (after holiday in Sweden).

Now, if you had the Firefox plugin Operator installed, you would have my contact information show up in your FF toolbar, like this:

Note the ‘Export Contact’ button in the toolbar. This will automatically create a vCard which I can directly open in my address book (I use the KDE addressbook). Very nice integration!

Now, I already asked the author how the plugin could be extended to support chemical microformats. Just think of the feature “Export Molecule (137)” (e.g. to Bioclipse), when reading a HTML version of paper in one of the Project Prospect enabled journals :)

In reply to my comment, he wrote a follow up highlighting one of blog items linked above (thanx for that!). Accidentally, he also published my Gmail account and IP address, which was really just for the blog owner to see who did the comment, and not for the world to harvest. This is a moment I am not so happy that Peter’s blog is so popular ;) Peter, maybe be a bit more careful with copy/pasting next time.

Peter and Henry (still not in blogspace?) have been doing things along these lines for years now, often in different contexts. But getting these things going is a bit trickier. Actually, the take up of the chemical microformats has been limited, and at least one alternative mechanism is being used: put the InChI in the @alt attribute on the <img> element. Other alternatives are possible too, such as recognizing molecules (or whatever else) based on a link to wikipedia; linking to entries in wikipedia is popular in Chemical blogspace.

One problem in getting microformats accepted, especially among chemists, is to have tools available. Tools meaning dedicated plugins for blogging software to easy adding microformats to a blog item. You’d be suprised how uncommon raw HTML editing has become in the last 10 years. ::: Structured Blogging ::: is a provider of such tools. On the using site, there is this nice Firefox plugin, that can extract information available in microformats, though Firefox3 is supposed to support some microformats natively.

Just today, Peter also blogged about a Berner-Lee’s presentation with the nice circular phenomena in all these web technologies. The diagrams nicely visualize the complex social aspects of these new technologies. (I’m sure the apply to chemoinformatics too… who makes a chemoinfo variant?) RDF is the way to go; it’s the machine interpretable (well, more accurate) microformat. All sorts of information is getting available as RDF. For example, check out bibtex2rdf, Wikipedia as RDF, uniprotRDF, and BioGUID. Moreover, GRDDL might mave this even more common. I have been maintaining a bookmark list of RDF things happening, check it out, the list is social and using microformats.

Any incorporation of content other than images and free text requires some HTML knowledge, but this can be rather limited. It is up to us chemoinformaticians to write good documentation on how to do things; so here is a first go.

Including CML in blogs and other RSS feeds

I blogged about including CML in blogs last February, and can generally refer to this article published last year: Chemical markup, XML, and the World Wide Web. 5. Applications of chemical metadata in RSS aggregators (PMID:15032525, DOI:10.1021/ci034244p). Basically, it just comes down to putting the CML code into the HTML version of your blog content, though I appreciate the need for plugins.

Including SMILES, CAS and InChI in blogs

Including SMILES is much easier as it is plain text, and has the advantage over InChI that it is much more readable. Chris wondered in the KinasePro blog on how to tag SMILES, while Paul did the same on ChemBark about CAS numbers.

Now, users of PostGenomic.com know how to add markup to their blogs to get PostGenomic index discussed literature, website and conferences. Something similar is easily done for chemistry things too, as I showed in Hacking InChI support into postgenomic.com (which was put on lower priority because of finishing my PhD). PostGenomic.com basically uses microformats, which I blogged about just a few days ago in Chemo::Blogs #2 , where I suggested the use of <span class="chemicalcompound">asperin</span>.

And this is the way SMILES, CAS and InChI’s can be tagged on blogs. The <span> element is HTML code to indicate a bit of similar content in HTML, and can, among many other things, be formatted differently than other text. However, this can also be used to add semantics in a relatively cheap, but accepted, way. [Microformats](http://microformats.org/ are formalized just by use, so whatever we, as chemistry bloggers, use will become the de facto standard. Here are my suggestions:

• for SMILES: <span class="smiles">CCO</span>
• for CAS registry numbers: <span class="casnumber">50-00-0</span>
• for InChI: <span class="inchi">InChI=1/CH4/h1H4</span>

The RDFa alternative

The future, however, might use RDFa over microformats, so here are the RDFa equivalents:

• for SMILES: <span class="chem:smiles">CCO</span>
• for CAS registry numbers: <span class="chem:casnumber">50-00-0</span>
• for InChI: <span class="chem:inchi">InChI=1/CH4/h1H4</span>

which requires you to register the namespace xmlns:chem="http://www.blueobelisk.org/chemistryblogs/" somewhere though. Formally, the URN for this namespace needs to be formalized; Peter, would the Blue Obelisk be the platform to do this? BTW, this is more advanced, and currently does not have practical advantages over the use of microformats.