First, let me note that if I would have to name a favorite molecule, and it was acetic acid, not ascorbic acid. Reason why it would be my favorite is acetic acid was the first organic molecule I put in the Woordenboek Organische Chemie in 1995.

We discussed a number of things, regarding the things we do. One of these was tagging molecules. Ian used http://rdf.openmolecules.net/?info:inchi/InChI=1/CH4/h1H4 instead of http://rdf.openmolecules.net/?InChI=1/CH4/h1H4. The first was not yet picked up by rdf.openmolecules.net but I fixed that.

We also discussed linking molecular structures with scientific literature. The discussions in blogspace of this week show that doing that by using computer programs is not appreciated by publishers (see here, here , here , here , here, and here ) (The publishers seem to prefer to like to send of a PDF to India or China.)

I proposed that the InChI would be part of the publication, for all molecules mentioned in the article. If a journal can require exact bibliography and experimental section formats, they can certainly require InChIs too. There are few programs left which cannot autogenerate an InChI, and the chemists draws the structures anyway. However, the software used in the editorial process does not support linking InChIs with a PDF (if that software would have been opensource …).

So, the best current option seems to be social tagging mechanisms, and this is what we talked about. Just use Connotea (or any other service) and tag your molecule with a DOI:

and

This tagging is done manually. No machines involved in that. Nothing the publishers can do about this. No ChemRefer needed. But this will allow us to start building a database with links between papers and molecules, which we badly need. BTW, we will not have to start from scratch. The NMRShiftDB already contains many links, which is open data!

Now, you might notice the informal semantics of the doi: prefix. That’s something I hereby propose, as it allow services to pick up the content more easily. You might also note the incorrect DOI in Connotea. The reason for that is that Connotea does not yet support a ‘/’ in a tag. I reported that problem.

The trick I use, is that the rdf.openmolecules.net gives every molecule a unique HTTP URL. This simply web2.0 approach offers an enormous amount of possibilities. The simplest application is that you can tag your molecules with a set label, such as my-tomato-set; after all, Connotea is account based. In this way, you can do open notebook QSAR studies (though the activities would still be missing).

The aforementioned example, however, give two classifications. Methane is an alkane and Methane is a gas (at room temperature). Not very well determined semantics, but it is web2.0, not the semantic web.

Interestingly, given some loosely defined semantics, use Connotea to link a molecule to a certain publication. For example, I can define Estrone is cited in the article with PubMed ID 15659855 using the tag pmid:15659855. I’m sure using the DOI would work too, using the tag doi:10.1107/S0108768104028344. I have not used these informal semantics in the rdf.openmolecules.net website yet, but if there is such interest, I can have such functionality hacked in minutes.

BTW, did anyone see Gene Ontology terms being used in social bookmarking services? For example, seeing a link to the PDB database with a tag go:0008152? Would be a bit cryptic, and, really, in this case rather minimalistic on information.

What’s next?

Now comes the tedious task of converting the QSAR data sets I used in my PhD research with these tags. It’s really something I wanted to do for a while now. Next on my TODO list is the Greasemonkey script that adds the tags from Connotea to PubChem.

Now, Nascent wrote that Nature is setting up Nature Precedings, which was earlier noted by Pedro. The official announcement was published as an editorial in Nature. This being a Nature initiative, and not focused on just chemistry, I am sure it will do better than CPS. BTW, media coverage is tracked in a social way.

I might request an test account; I do have an old half-finished manuscript that I never got around to finishing. While still relevant, it could use some community input; this preprint server would be the perfect tool. That’s how my first manuscript ended up on CPS too :)

Searching

Searching literature is traditionally done in systems like Chemical Abstracts and Web-of-Science. The open nature of a growing number of repositories (e.g. the Dutch DARE) and indexing facilities like PubMed make these proprietary tools obsolete.

It is incorrect to assume that these payed services are the only trustworthy sources. Even WoS fails to make the all links between entries in the database. For example, I am aware of two missing citations to articles I have written, even though both the cited and the citing article is available in the system. One of the citing articles was in the Angewandte Chemie!

Additionally, some search services, like Google Scholar, have the advantage that they find copies and close variants of articles in proprietary articles on home pages and in open repositories. Today, I learned about Scientific Commons which indexes and links to a staggering 1.5M publications, using, among others, PubMed and university repositories. Where possible it makes direct links to PDF versions of the article.

Ranking

Mitch set up ChemRank, to which Peter , the ChemBlog and I replied . Afterwards, I learned that other services are available too, that allow, in addition to setting up an online personal literature database, voting and commenting on articles.

Apparently, CiteULike (CUL) supports this too. In contrast to ChemRank, CUL requires a login, which I personally see as an advantage, because I can browse literature bookmarked by other accounts I trust. There is also Connotea but I never liked that site that much (e.g. is allows bookmarking any web page); Rich has his comments too . I would also like to mention BioWizard which is based on the PubMed content, which actually covers a good deal of chemistry literature nowadays too.

Local Storage

These above mentioned systems can be used as alternative to offline bibliographic database systems, like EndNote and JabRef. The latter is my favorite, being based on BibTeX which I use for my LaTeX based publications, and is opensource and contains a few patches from yours truly. Jungfreudlich wondered how people organized their PDF archive and I commented how I do it:

• a directory hierarchy based on journal name and year
• file names that include last name of the first author and year
• JabRef for the bibiographic database
• Strigi for full text search

Jörg and the power of goo replied too.

Mashups

I have accounts on several online tools now (with some duplication which I don’t like), and I have no idea which of the options will stay around. Time will learn. Good news is that the open characters of many of these allow making mashups, and generally integrate tools. For example, JabRef allows downloading citations from PubMed, and Noel suggested to use Greasemonkey scripts to link to the supplementary information for his articles, instead of using the mechanisms journals have. I can see the advantage of this, as, for example, Wiley takes full copyright of the data in SI material , while Noel’s mechanism would keep the data open.

For now, however, I would very much like to see a meta service where I can query rankings and comment for articles using any or all of the above tools.

But, when I tried to create a new group, the system fails. I promised me to send me email for confirmation. Tried it twice via my Sourceforge email account. No email. I then changed my email for my Nature account to my Gmail address. Still no email…

I am not located in Boston or London, is that the problem? Is being ‘global’ not good enough? Is the requirement to have two ‘o’s in the name? Cologne then, maybe?

(Missing) Features

For the rest, the system seems interesting. I am not too fond of having to create accounts all over the place (what was the password again???), but looks promising. The thing I missed most when filling out my profile was a feature to import the list of my publications from Connotea.

Another thing I missed, was the ability to mention my blog(s) in my profile. May I put this in as request too? BTW, is there a group or forum on Nature Network where I can file these things?

For the KDE desktop Kat has for more than a year offered this, and latter Kerry came along as frontend to [Beagle(http://beaglewiki.org/Main_Page)], though this does not have the nice integration with KDE kfile plugins. Since then, Kat developed has come to a stop (unfortunately), and attempts to reach the main author (Roberto) have been unsuccesfull. Last thing happening was a rewrite of the database backend.

Additionally, Scott Wheeler proposed Tenor on FOSDEM 2005: “KDE 4: Beyond Hierarchical Data, The Desktop as a Searchable Web of Context”. A semantic desktop; potentially cool, but I have heard little from it lately, except for some rumours that Scott has some actual code at home.

Now, Strigi (download) has come along, with a fast indexing engine, just the thing where the Kat developed seemed to have stopped. The design is different from that of Kat, but it does not seem unlikely that Kat code can be ported. No support for PDF or OpenOffice.org documents yet, but that’s really the easy part, and kfile is on its way.

Getting back to Tenor, one might wonder how Strigi could implement Tenor concepts. A simple approach is at least to allow users to tag files, just like we have become used to with blogs (e.g. Technorati.com) and websites (e.g. Connotea). This could be easily implemented using extended attributes (xattr), already used by Beagle :

# file: home/egonw/1CRN.jpg
user.Tenor.Keywords="crambin"
user.Tenor.Comment="Used in my ontologies presentation."

Obviously, this example shows not just these tags, but a user comment too. The idea, here, is that Strigi mines these attributes in addition to the file itself, so that search on tags can be done too. BTW, my argument to use this, instead of putting these things in the Strigi database itself, is persistence: data and metadata are kept together. KDE’s file properties dialog would be extended with an extra tab that allows editing these fields.

Strigi itself can be embedded in KDE applications to search specific information (e.g. search molecular data within Kalzium using the InChI), and even in the FileOpen dialog. We need patches for KDE4 that allows this, soon.