Chemical datuments as scientific enablers by Henry S Rzepa. (Journal of Cheminformatics 2013, 5:6 doi:10.1186/1758-2946-5-6)
Abstract:
This article is an attempt to construct a chemical datument as a means of presenting insights into chemical phenomena in a scientific journal. An exploration of the interactions present in a small fragment of duplex Z-DNA and the nature of the catalytic centre of a carbon-dioxide/alkene epoxide alternating co-polymerisation is presented in this datument, with examples of the use of three software tools, one based on Java, the other two using Javascript and HTML5 technologies. The implications for the evolution of scientific journals are discussed.
From the background:
Chemical sciences are often considered to stand at the crossroads of paths to many disciplines, including molecular and life sciences, materials and polymer sciences, physics, mathematical and computer sciences. As a research discipline, chemistry has itself evolved over the last few decades to focus its metaphorical microscope on both far larger and more complex molecular systems than previously attempted, as well as uncovering a far more subtle understanding of the quantum mechanical underpinnings of even the smallest of molecules. Both these extremes, and everything in between, rely heavily on data. Data in turn is often presented in the form of visual or temporal models that are constructed to illustrate molecular behaviour and the scientific semantics. In the present article, I argue that the mechanisms for sharing both the underlying data, and the (semantic) models between scientists need to evolve in parallel with the increasing complexity of these models. Put simply, the main exchange mechanism, the scientific journal, is accepted [1] as seriously lagging behind in its fitness for purpose. It is in urgent need of reinvention; one experiment in such was presented as a data-rich chemical exploratorium [2]. My case here in this article will be based on my recent research experiences in two specific areas. The first involves a detailed analysis of the inner kernel of the Z-DNA duplex using modern techniques for interpreting the electronic properties of a molecule. The second recounts the experiences learnt from modelling the catalysed alternating co-polymerisation of an alkene epoxide and carbon dioxide.
Effective sharing of data, in scientific journals or no, requires either a common semantic (we know that’s uncommon) or a mapping between semantics (how may times must we repeat the same mappings, separately?).
Embedding notions of subject identity and mapping between identifications in chemical datuments could increase the reuse of data, as well as its longevity.