Raiding Chemistry's Data Tombs

Rich Apodaca — Mon, 04 Feb 2008 11:46:00 +0000

Duncan Hull offers an interesting commentary on the rapid increase in the number of biologically-oriented databases. He asks whether all of this abundance is leading to nothing more than a bad case of data indigestion, in which data is dumped into write-only "data tombs," never to be seen again.

A data tomb is created whenever the ability to generate data outstrips the ability to do useful things with it. Like the burial tombs of ancient civilizations, data tombs are created for many reasons and take many forms.

Where are chemistry's data tombs and what do they look like? Given that the number of free chemistry databases pales in comparison to the number free biological databases, the question may seem irrelevant.

Nevertheless, data tombs in chemistry are ubiquitous. The most obvious examples are the supplementary data sections of major chemical journals. These write-only databases suffer from dual afflictions of copyright restriction and electronic degradation.

The collective experimental sections of the world's chemical literature is, in effect, a vast catacomb of jealously-guarded, but poorly-catalogued treasures.

Data silos are an especially prevalent kind of data tomb that result when data is created for a single use and either for technical or political reasons never placed in a real database. SD files containing SAR data, PowerPoint slides containing tables of synthetic yields, and Word documents containing experimental procedures are some of the forms these chemical data silos take.

What chemical data tombs have you run into, and what methods did you use to raid them?

Image Credit: Duncan Hull

Rethinking Chemistry Publications: Nature Protocols Makes the Experimental Section a First-Class Citizen

Rich Apodaca — Mon, 10 Sep 2007 09:35:00 +0000

Experimental procedures are strange beasts. Loathed (at least temporarily) by those who must prepare them yet central to science, the lowly experimental section is mostly forgotten in the daily struggle of publish or perish. Abstracts, discussions, and conclusions will probably be useless 20 years from now, at least in chemistry. In contrast, the experimental section (and the tables based on them) may well live forever.

It was from this perspective that I was fascinated to learn about Nature Protocols from thescepticalchymist. From the website:

Nature Protocols is an online resource for protocols, including authoritative, peer-reviewed 'Nature Protocols' and an interactive 'Protocols Network'. The two create a dynamic forum for scientists to upload and comment on protocols.

Experimental protocols may be poised to make a comeback in the world of scientific publication. Specifically two chemistry protocols caught my eye:

Unlike most publications in which the experimental section is treated as an afterthought, in Nature Protocols, the experimental section occupies center-stage. Richly annotated and hyperlinked descriptions are complimented by full-color images. Videos have also begun to appear.

Many modern chemistry journals have either abandoned the experimental section altogether or simply downplay it to the point of making it far less useful than it could be. This might have made sense when paper was the primary means of distributing scientific content. With digital storage capacity now routinely measured in terabytes and long-tail scientific economics in full force, this position makes little sense today. The information-delivery platform has changed forever; to what degree will this change the nature of what gets communicated?

image credit: Donohoe and Thomas, Nature Protocols

Depth-First: Tag experimentalsection

Raiding Chemistry's Data Tombs

Rethinking Chemistry Publications: Nature Protocols Makes the Experimental Section a First-Class Citizen