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.

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:

This article not subject to U.S. Copyright. Published xxxx by the American Chemical Society

As far as I can tell, this article is not part of the ACS AuthorChoice program.

As chemical informatics continues its climb out of a decades-long stagnation, the number of free chemical databases continues to grow. But despite all the activity, reaction databases are notably under-represented. For this reason, I was delighted to stumble onto Boston University's Center for Chemical Methodology and Library Development Reaction Database (CMLD-BU).

According to their website, CMLD-BU:

...is a new center funded by the National Institute of General Medical Sciences ( NIGMS ) focused on the discovery of new methodologies to produce novel chemical libraries of unprecedented complexity for biological screening. The goal of the CMLD-BU is to explore and expand the diversity of small-molecule libraries by creating general, useful protocols for stereocontrolled synthesis. ... A major objective of the CMLD-BU is also to provide information and chemistry protocols to the public on parallel and chemical library synthesis. ...

Use this link to begin exploring their service. To date the CMLD-BU has deposited just over 1,600 Substances with PubChem and their site shows 125 reaction protocols.

Although CMLD-BU's user interface could use some tweaking, their content is right on the money: real examples of preparative reactions with links to the primary literature and even spectral data.

Are we at the end of this process or at the beginning? Only time will tell. But the nearly infinite shelflife and ubiquity of chemical information coupled with the inexorable approach of virtually zero-cost computer services leaves only one of those two possibilities worthy of serious consideration.

Although I still don't use it yet, Connotea is a very useful service for many scientists. Combining aspects of social networking and bibliography management, Connotea offers a glimpse at some of the vast potential for Web 2.0 in the sciences. But the service is not without its thorny technical problems, one of which is discussed in this article.

For those unfamiliar with the service, Connotea lets you organize and share hyperlinks. This, in itself, is nothing remarkable. Many services such as Digg, del.icio.us, and Reddit offer similar capability.

What's unique about Connotea is its emphasis on bookmarking scientific and scholarly content. By taking advantage of the CrossRef service built on top of the DOI system, Connotea makes creating a bibliographical reference to a paper as easy as entering a short alphanumeric sequence found on the document itself.

As long as all Connotea users work with DOIs, there is no problem. The DOI organization ensures that every document with a DOI can be accessed via a single, immutable URL. For example, if a paper has a DOI of "10.1021/ol015948s", then the document can be accessed through this link.

But what happens if a Connotea user either doesn't know about DOI or for some reason prefers not to use it? Instead, they'd rather work with a publisher's URL directly. This is not as unlikely as it may seem at first. For example, Connotea fails to recognize the title of many ACS papers when they are entered as DOIs, but does recognize them as direct abstract links.

PubMed offers still more ways to refer to the same document. To name a few:

• Abstract
• Abstract Plus
• Citation

Without really trying, we've found no fewer than five different URLs that all refer to the same scientific work. If you look under my user profile, you'll see that Connotea is happy to add all of these references as separate entities. This means that each will receive its own set of tags and its own summary page. If my collection of links grows to a few hundred, I may not realize that I actually have two or three links to the same paper in my collection. And other Connotea users may fail to see my papers because they're using a URL that differs from mine.

After researching this problem a bit, I found that although it doesn't seem to have an immediate solution, at least it has a name: Buggotea. It bears a remarkable similarity to the "unique" SMILES problem, which was a major motivation for the development of InChI.

It wasn't long ago that the ability to access the scientific literature online seemed far-fetched. Today, the Internet as become the only scientific publication medium that matters. This has created a variety of new problems - and opportunities to solve them.

Image Credit: gottcha78