Semantics Chemistry

There is a lot of confusion over the meaning of the terms theoretical chemistry, computational chemistry and molecular modelling. Indeed, many practitioners use all three labels to describe aspects of their research, as the occasion demands "Theoretical chemistry is often considered synonymous with quantum mechanics, whereas computational chemistry encompasses not only quantum mechanics but also molecular mechaiucs, minimisation, simulations, conformational analysis and other computer-based methods for understanding and predicting the behaviour of molecular systems. Molecular modellers use all of these methods and so we shall not concern ourselves with semantics but rather shall consider any theoretical or computational tecluiique that provides insight into the behaviour of molecular systems to be an example of molecular modelling. If a distinction has to be... 

Web in the life of the medicinal chemist. One may see the development of alerting services for the primary medicinal chemistry journals. The Web-based information search process could be replaced by a much more structured one based on metadata, derived by automated processing of the original full-text article. To discover new and potentially interesting articles, the user subscribes to the RSS feeds of relevant publishers and can simply search the latest items that appear automatically for keywords of interest. The article download is still necessary, but it may be possible for the client software to automatically invoke bibliographic tools to store the found references. Another application of the Chemical Semantic Web may be as alerting services for new additions to chemical databases where users get alerts for the new additions of structures or reactions. 

When supramolecular chemistry emerged at the forefront of science, it embodied colloid chemistry as one of its facets. A semantic boundary exists between supramolecular chemistry and colloids, as the former involves design logistics a priori in addition to preselected synthetic strategies. The simplest kind of colloidal... 

In the older papers the inaccurate old word carbonium ion, which originated from organic chemistry, has not been replaced by the semantically correct term carbenium ion. The appearance of this term marks the time when Olah s discovery of quinquevalent carbon in super-acid solution, the true carbonium ion, made the change of nomenclature essential and urgent. 

As a human trained in chemistry, you probably understand much of the semantics, but consider how much potential ambiguity and implied meaning is contained in this admittedly concise statement. 

The possibilities and application of the Semantic Web to chemistry were initially identified by Murray-Rust and Rzepa (1999, 2000 Rzepa and Murray-Rust 2001) and have been promoted in a number of papers since. The precondition to the Semantic Web, the maintenance of data within XML format, has become a reality, whereas the representation of the data within XML has been subject to evolution in the last few years. For example, the SVG format for holding graphics as XML was initially promising, but adoption never took off beyond a few examples. As Adobe is no longer developing and supporting the format, it can be regarded at present as an evolutionary dead end. 

In this chapter we shall first describe RDF and OWL, the grammar of the Semantic Web, and then move on to identifiers, the vocabulary of the Semantic Web, and ontologies, which represent the real-world knowledge required to make use of the grammar and vocabulary. We will concentrate on practical chemistry- and biochemistry-orientated deployments of Semantic Web technology rather than the computer science behind it. Then we will cover some case studies Web services, databases, and semantic publishing in the forms of Semantic Eye and RSC Project Prospect. We will briefly cover what the Semantic Web has to offer for experimental data before finishing up with some possible future directions. 

The main application areas of Semantic Web technology to chemistry so far have been in Web services, especially PubChem, chemical databases, and publishing. 

One important application of Web services is in distributing computational effort over many different machines, creating what in the UK is called a grid, or in the cases we are about to mention, a semantic grid. We shall briefly describe two research projects in the UK that have applied this to the field of chemistry, in Southampton and Leeds, respectively. 

Chemistry is some way behind the biomedical sciences in standardization of research protocols. The MIBBI (Minimum Information for Biological and Biomedical Investigations) Project (MIBBI Consortium 2008) aims to bring the various Minimum Information protocols for different sorts of biomedical experiments into line with one another and oversees over a dozen protocols. The mapping of the protocols themselves to stable Semantic Web identifiers is achieved through an ontology. 

Restricting ourselves to the short-term future, where will the Semantic Web be in two years with respect to chemistry ... 

Note Chemistry has been variously defined, to the point where definition has become a semantic exercise of questionable, if not negative, value. Chemistry is the science of matter and Chemistry is a branch of physics are two instances of such definitions. The first relegates physics to the background while the second accords it supremacy. 

This contribution as a chapter in the special volume of ADVANCES IN QUANTUM CHEMISTRY on Confined Quantum Systems is focussed on (i) the hydrogen atom, (ii) confinement by conoidal boundaries, and (iii) semi-infinite spaces however, some of its discussions may extend their validity to other physical systems and to confinement in closed volumes. The limitations in the title are given as a point of reference, and also take into account that several of the other chapters deal with confinement in finite volumes. A semantic parenthesis is also appropriate and self-explanatory Compare conical curves (circles, ellipses, parabolas, hyperbolas and their radial asymptotes) with conoidal surfaces (spheres, spheroids, paraboloids, hyperboloids and their radial asymptotic cones). 

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