Name to structure conversion

Fig. 1.16 lUPAC name to structure conversion in Marvin View... 

Nowadays, thanks to the availability, cost, and ease-of use of chemical structure databases, many of these text databases have been converted into a structure format, and most chemical databases are now structure searchable. A simple search of the Internet will show that many databases still lack chemical structures and therefore are not searchable by structure in the original format, for example, an online HTML page. These pages, however, can contain valuable information and, with the application of the appropriate name-to-structure (N2S) conversion tools can be made searchable. 

The first publication about the computer translation of chemical names was published by Garfield in 1961. In that article, he described the conversion of names into chemical formulas and initiated the path toward N2S algorithm development.45 Developments in 1967 at CAS provided internal procedures for the automatic conversion of CAS names into chemical diagrams.46 47 The first commercially available software program was CambridgeSoft s Name=Struct released in 1999,48 now patented,49 which was followed shortly by ACD/Labs ACD/Name to Structure product released in 2000.50 Two more commercial products are available Chemlnnovation s NameExpert51 and... 

OpenEye s Lexichem,23 and ChemAxon52 has announced the imminent release of their own product early in 2008. As mentioned earlier, an Open Source Java library for the interpretation of IUPAC systematic names,34 OPSIN, has also been made available. In this chapter, most examples are based on Name=Struct and ACD/Name to Structure. We judge these programs to currently be the most advanced products in this area, but all considerations are general in nature and relevant to all of the conversion routines presently existing or still under development. 

Figure 3.6 shows 12 structures that may correspond to the abbreviation DPA. Six of them can be output by the ACD/Name to Structure software package, and six more were found by browsing the Internet. Note that even a specific context cannot guarantee an exact meaning. For example, both structures 3 and 8 were found in publications about coordination compounds. In general, chemical abbreviations are not unique and can rarely be distinguished from other trivial names except for the rather weak criterion that all letters are capitalized. We can conclude that conversion of any trivial name shorter than about five or six characters is not safe. A few rarer exceptions do exist, but this is a very short list. Examples include reserved abbreviations such as those for dimethyl sulfoxide (DMSO) and ethylenediaminetetraacetic acid, EDTA. 

Thus, the conversion of chemical names into structures consists of parsing the name into longest text fragments. These fragments are submitted to lexical analysis and the derived lexical units are compared with a collection of predefined units in a dictionary. 

Substantial attention and progress has been made in the development of procedures to effect conversion between chemical substance representations. Zamora and Davis [26] describe an algorithm to convert a coordinate representation of a chemical substance (derived from input by a chemical typewriter) to a connection table. An approach for interactive input of a structure diagram and conversion of this representation to a connection table suitable for substructure searching is discussed by Feldmann [27]. The conversion of systematic nomenclature to connection tables offers a powerful editing tool as well as a potential mechanism for conversion of name files to connection tables this type of conversion is described by Vander Stouw [28]. 

Ideally, every organic substance should have a completely descriptive, systematic name to permit only one structural formula to be written for it. This ideal has been approached closely in some of the current nomenclature systems but, unfortunately, truly systematic nomenclature for very complicated compounds is often hopeless for conversational or routine scripto-rial purposes. As a result, we will at times resort to using (common) trivial names, especially if it is impractical to do otherwise. Clearly, the description 9-(2,6,6-trimethyl-l-cyclohexenyl)-3,7-dimethyl-2,4,6,8-nonatetraen-J-ol has phonetic disadvantages as a handy name for vitamin A ... 

Names like this are fine for familiar compounds that are widely used and referred to by chemists, biologists, doctors, nurses, perfumers alike. But there are over 16 million known organic compounds. They can t all have simple names, and no one would remember them if they did, For this reason, the IUPAC (International Union of Pure and Applied Chemistry) have developed systematic nomenclature, a set of rules that allows any compound to be given a unique name that can be deduced directly from its chemical structure. Conversely, a chemical structure can be deduced from its systematic name. 

Our intention in this chapter is to examine the challenges of extracting identihers from chemistry-related documents and the conversion of those identihers into chemical structures. The authors of this work each have well over a decade of experience in chemical structure representation and systematic nomenclature. We have been deeply involved in the development of software algorithms and software for the generation of systematic names and the conversion of chemical identihers into chemical structures.9 Although we have our own biases concerning approaches to the problem of N2S conversion, we have done our utmost to be objective in our review of the subject and comparison of approaches and performance. 

The conversion of systematic names to their chemical structures is a time-consuming, skill-intensive process, and is not a minor undertaking. Such a project is guaranteed to take many years of development to cover the most important nomenclature operations. 

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