Semantics

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... 

The syntax and semantics of the typing rules in a chem.rul file are included in the HyperChem Reference Manual. The following example illustrates their use. The five AMBER types for oxygen atoms shown above are defined in chem.rul by the following rules ... 

Two-Dimensional Representation of Chemical Structures. The lUPAC standardization of organic nomenclature allows automatic translation of a chemical s name into its chemical stmcture, or, conversely, the naming of a compound based on its stmcture. The chemical formula for a compound can be translated into its stmcture once a set of semantic rules for representation are estabUshed (26). The semantic rules and their appHcation have been described (27,28). The inverse problem, generating correct names from chemical stmctures, has been addressed (28) and explored for the specific case of naming condensed benzenoid hydrocarbons (29,30). 

The distinction between these two classes of reactions is semantic for the five-membered rings Diels-Alder reaction at the F/B positions in (269) (four atom fragment) is equivalent to 1,3-dipolar cycloaddition in (270) across the three-atom fragment, both providing the 47t-electron component of the cycloaddition. Oxazoles and isoxazoles and their polyaza analogues show reduced aromatic character and will undergo many cycloadditions, whereas fully nitrogenous azoles such as pyrazoles and imidazoles do not, except in certain isolated cases. 

A note on semantics a function is a prescription for producing a number from a set of variables (coordinates). A functional is similarly a prescription for producing a number from a function, which in turn depends on variables. A wave function and the electron density are thus functions, while an energy depending on a wave function or an electron density is a functional. We will denote a function depending on a set of variables with parentheses,/(x), while a functional depending on a function is denoted with brackets,... 

Chemists communicate in a highly elaborated alfabetic [sic] and symbolic language. The chemical nomenclature is a predominant literary language. Only short names are spoken, the official, sometimes very long terms are replaced by trivial names or are uncanonically abbreviated for oral communication. The chemical nomenclature works with a distinct syntax and semantic, but is not suited for textual sentences. Structures are drawn according to specific rules. 

Bartsch, R. (1998). Dynamic Conceptual Semantics. CSLl Publications FOLLl. 

We have developed a system based on SNOW-MED to extract medical information from herbal texts. SNOW-MED is a semantic index that recognizes relationships between groups of words [26], For example, the semantic map for thrush is related to yeast, infection, and microbe. Although this system may eventually allow a potential pharmacological function to be extrapolated, we are currently using the system to simply extract disorders from the text. We have used the Mayo Vocabulary Server to perform this data mining [34, 35]. 

Gardner SP. Ontologies and semantic data integration. Drug Discov Today 2005 10 1001-7. 

Feldman R, Regev Y, Hurvitz E, Finkelstein-Landau M. Mining the biomedical literature using semantic analysis and natural language processing techniques Biosilico 2003 1 69-80. 

Hendler J, Berners-Lee T, Miller E. Integrating applications on the semantic web. J Inst Elect Eng lapan 2002 122 676-80. 

Murray-Rust P, Rzepa HS. Towards the chemical semantic web. An introduction to RSS. Internet J Chem 2003 6 Article 4. 

It is also worth mentioning the future development of the Web for chemical information purposes. The emergence of the Semantic Web [5] in general and the Chemical Semantic Web [6] in particular would further the roles of the... 

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. 

Gkoutos GV, Murray-Rust P, Rzepa HS, Wright M. Chemical markup, XML, and the World-Wide Web. 3. Toward a signed semantic chemical web of trust. J Chem Inf Comput Sci 2001 41(5) 1124-30. 

Besides the flat set of terms we also use and extract thesaurus relations such as synonymy , broader term and narrower term . By introducing these relationships we create a thesaurus from our terminology. The semantic knowledge encoded in the thesaurus is used for expansion of queries within the KSP and also for enriching the UltraLink. 

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